Publications

(opens in a new window)Cell State Transition Models Stratify Breast Cancer Cell Phenotypes and Reveal New Therapeutic Targets. Rukhlenko O and Imoto H et al. Cancers (Basel). 2024 June 27

Genomic and Transcriptomic Analysis of a Patient with Early-Onset Colorectal Cancer and Therapy-Induced Focal Nodular Hyperplasia: A Case Report. O'Reilly M et al. Journal of Personalized Medicine. 2024 June 15

(opens in a new window)A novel TCF3::PIK3R1 fusion linked to decreased PI3K-AKT signalling activity in paediatric B-acute lymphoblastic leukaemia. Grady E et al. British Journal of Haematology. 2024 June 14

(opens in a new window)BTLA and PD-1 signals attenuate TCR-mediated transcriptomic changes. Arifin MZ et al. iScience. 2024 June 12

(opens in a new window)Effect of hypercholesterolemia on circulating and cardiomyocyte-derived extracellular vesicles. Kovacshazi C et al. Scientific Reports. 2024 May 26

(opens in a new window)Hypoxia-inducible factor-driven glycolytic adaptations in host-microbe interactions. DeMichele E et al.  Pflügers Archiv - European Journal of Physiology. 2024 April 4

(opens in a new window)Multimodal, Technology-Assisted Intervention for the Management of Menopause after Cancer Improves Cancer-Related Quality of Life-Results from the Menopause after Cancer (Mac) Study. Donohoe F et al. Cancers (Basel). 2024 March 12

(opens in a new window)Managing Menopause After Cancer. Hickey M et al. The Lancet. 2024 March 5

(opens in a new window)Multiple Myeloma Derived Extracellular Vesicle Uptake by Monocyte Cells Stimulates IL-6 and MMP-9 Secretion and Promotes Cancer Cell Migration and Proliferation. Sheridan R et al. Cancers (Basel). 2024 February 29

(opens in a new window)Paralog dispensability shapes homozygous deletion patterns in tumor genomes. De Kegel B and Ryan CJ. Molecular Systems Biology. 2023 November 14

(opens in a new window)Recommendations from the COST action CA17116 (SPRINT) for the standardization of perinatal derivative preparation and in vitro testing. Janev A et al. Frontiers in Bioengineering and Biotechnology. 2023 November 14

(opens in a new window)Transcriptional profiling of early differentiation of primary human mesenchymal stem cells into chondrocytes. Schwarzl T et al. Scientific Data. 2023 November 3

(opens in a new window)Targeting hypoxia-inducible factor-1 alpha suppresses Helicobacter pylori-induced gastric injury via attenuation of both cag-mediated microbial virulence and proinflammatory host responses. Noto J et al. Gut Microbes. 2023 October 13

(opens in a new window)Integrated analysis of transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders. Matveeva A et al. Amyotroph Lateral Scler Frontotemporal Degener. 2023 October 1

(opens in a new window)Cell state transition analysis identifies interventions that improve control of M. tuberculosis infection by susceptible macrophages. Yabaji S et al. Science Advances. 2023 September 27

(opens in a new window)Radiomics-based prediction of FIGO grade for placenta accreta spectrum. Bartels H et al. European Radiology Experimental. 2023 September 20

(opens in a new window)Hypoxia induces a glycolytic complex in intestinal epithelial cells independent of HIF-1-driven glycolytic gene expression. Kierans S et al. PNAS. 2023 August 29

(opens in a new window)Proteomic Mapping of the Interactome of KRAS Mutants Identifies New Features of RAS Signalling Networks and the Mechanism of Action of Sotorasib. Nolan A et al. Cancers. 2023 August 17

(opens in a new window)A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression. Imoto H et al. Biomolecules. 2023 August 2

(opens in a new window)Kinase Suppressor of RAS 1 (KSR1) Maintains the Transformed Phenotype of BRAFV600E Mutant Human Melanoma Cells. Liu Z et al. International Journal of Molecular Sciences. 2023 July 23

(opens in a new window)Cyclophilin A Isomerisation of Septin 2 Mediates Abscission during Cytokinesis. Gorry R et al. International Journal of Molecular Sciences. 2023 July 4

(opens in a new window)Carcinoma of unknown primary (CUP): an update for histopathologists. Beauchamp K et al. Cancer and Metastasis Reviews. 2023 July 3

(opens in a new window)The protein and miRNA profile of plasma extracellular vesicles (EVs) can distinguish feline mammary adenocarcinoma patients from healthy feline controls. Howard J et al. Scientific Reports. 2023 June 6

(opens in a new window)Deciphering the tumour immune microenvironment cell by cell. Nabhan M et al. Immuno-Oncology and Technology. 2023 June

(opens in a new window)Reversing pathological cell states: the road less travelled can extend the therapeutic horizon. Kholodenko B et al. Trends in Cell Biology. 2023 May 30

(opens in a new window)Small gene networks delineate immune cell states and characterize immunotherapy response in melanoma. Egan D et al. Cancer Immunology Research. 2023 May 25

(opens in a new window)Structure-based prediction of Ras-effector binding affinities and design of "branchegetic" interface mutations. Junk P and Kiel C. Structure. 2023 Apr 28

(opens in a new window)Interactome dynamics of RAF1-BRAF kinase monomers and dimers. Iglesias-Martinez LF et al. Scientific Data. 2023 Apr 12

(opens in a new window)Polycomb Alterations in Acute Myeloid Leukaemia: From Structure to Function. Bhattacharyya T and Bond J. Cancers (Basel). 2023 March 9

(opens in a new window)Analysis of context-specific KRAS–effector (sub)complexes in Caco-2 cells. Ternet C et al. Life Science Alliance. 2023 March 9

(opens in a new window)Unveiling the epigenomic mechanisms of acquired platinum-resistance in high-grade serous ovarian cancer. Silva R et al. IJC Cancer Genetics and Epigenetics. 2023 March 8

(opens in a new window)Targeting synthetic lethal paralogs in cancer. Ryan CJ et al. Trends in Cancer. 2023 March 6

(opens in a new window)Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma. Hastings JF et al. Science Advances. 2023 March 3

(opens in a new window)Whole-cell energy modeling reveals quantitative changes of predicted energy flows in RAS mutant cancer cell lines.Sevrin T et al.iScience.2023 Feb 17

(opens in a new window)B-cell and complement signature in severe hidradenitis suppurativa that does not respond to adalimumab. Hambly R et al.British Journal of Dermatology.2023 Jan 23

(opens in a new window)Oncotherapeutic Strategies in Early Onset Colorectal Cancer. O'Reilly M et al.Cancers(Basel). 2023 Jan 16

(opens in a new window)Dynamic Regulation of RAS and RAS Signaling. Kolch W et al.Biochemical Journal.2023 January 6

(opens in a new window)Disease–Gene Networks of Skin Pigmentation Disorders and Reconstruction of Protein–Protein Interaction Networks. D'Arcy C et al. Bioengineering. 2022 December 21

(opens in a new window)The HIF-prolyl hydroxylases have distinct and nonredundant roles in colitis-associated cancer. Harnoss JM et al. JCI Insight. 2022 November 22

(opens in a new window)Cell-based therapy in prophylaxis and treatment of chronic graft-versus-host disease. Doglio M et al. Frontiers in Immunology. 2022 November 17

(opens in a new window)Targeting KRAS in Pancreatic Cancer. Cowzer D et al. Journal of Personalized Medicine. 2022 November 8

(opens in a new window)Methods and criteria for validating the multimodal functions of perinatal derivatives when used in oncological and antimicrobial applications. Silini AR et al. Frontiers in Bioengineering and Biotechnology. 2022 October 13

(opens in a new window)Prolyl Hydroxylase Inhibition Mitigates Allograft Injury During Liver Transplantation. Harnoss JM et al. Transplantation. 2022 October 1

(opens in a new window)CRABP2 -- A novel biomarker for high risk endometrial cancer. Egan D et al. Gynecologic Oncology. 2022 September 24(opens in a new window)

Control of cell state transitions. Rukhlenko O et al. Nature. 2022 September 14

(opens in a new window)Perinatal derivatives: how to best validate their immunomodulatory functions. Papait A et al. Frontiers in Bioengineering and Biotechnology. 2022 September 14

(opens in a new window)Experimental reproducibility limits the correlation between mRNA and protein abundances in tumor proteomic profiles. Upadhya SW, Ryan CJ. Cell Reports Methods. 2022 September 8

(opens in a new window)Proteasomal down-regulation of the proapoptotic MST2 pathway contributes to BRAF inhibitor resistance in melanoma.boris Romano et al. Life Science Alliance. 2022 August 29

(opens in a new window)Interaction of LATS1 with SMAC links the MST2/Hippo pathway with apoptosis in an IAP-dependent manner. Garcia-Gutierrez L et al. Cell Death & Disease. 2022 August 8

(opens in a new window)Perinatal derivatives; how to best characterize their multimodal functions in vitro. Part C: Inflammation, Angiogenesis, and Wound Healing. Flores A et al. Frontiers in Bioengineering and Biotechnology. 2022 August 4

(opens in a new window)A Systems Biology Approach to Investigate Kinase Signal Transduction Networks That Are Involved in Triple Negative Breast Cancer Resistance to Cisplatin. Mukherjee N et al. Journal of Personalized Medicine. 2022 August 3

(opens in a new window)Hypoxia-inducible factor (HIF) as a bridge between healthy barrier function, wound healing, and fibrosis. Steiner CA et al. AJP Cell Physiology. 2022 August 1

(opens in a new window)Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells. Bokharaie H et al. Biomolecules. 2022 July 17

(opens in a new window)Prolyl Hydroxylase Inhibition Mitigates Allograft Injury During Liver Transplantation. Harnoss J et al. Transplantation. 2022 July 11

(opens in a new window)Machine learning based prediction and the influence of complement - Coagulation pathway proteins on clinical outcome: Results from the NEURAPRO trial. Susai SR et al. Brain, behavior and immunity. 2022 July 1

(opens in a new window)A comparative analysis of extracellular vesicles (EVs) from human and feline plasma. Howard J et al. Scientific Reports. 2022 June 27

(opens in a new window)The effect of HIF on metabolism and immunity. Cormac Taylor and Carsten Scholz. Nature Reviews Nephrology. 2022 June 20

(opens in a new window)Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling. Nolan A et al. Genes. 2022 April 10

(opens in a new window)Emerging RAS-directed therapies for cancer. Conroy M et al. Cancer Drug Resistance. 2022 April 8

(opens in a new window)Reconstruction and analysis of a large-scale binary Ras-effector signaling network. Catozzi S et al. Cell Communication and Signaling. 2022 March 4

(opens in a new window)Investigating a clinically actionable BRAF mutation for monitoring low-grade serous ovarian cancer: A case report. Silva R et al. Case Reports in Women's Health. 2022 February 6

(opens in a new window)Suppressive effects of the obese tumor microenvironment on CD8 T cell infiltration and effector function. Dyck L er al. Journal of Experimental Medicine. 2022 February 1

(opens in a new window)Clinico-biological features of T-cell acute lymphoblastic leukemia with fusion proteins. Steimle T et al. Blood Cancer Journal. 2022 January 26

(opens in a new window)HOMELETTE: a unified interface to homology modelling software. Philipp Junk, Christina Kiel. Bioinformatics. 2021 December 25

(opens in a new window)Can Systems Biology Advance Clinical Precision Oncology? Andrea Rocca, Boris N. Kholodenko. Cancers. 2021 December 16

(opens in a new window)Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI. Degasperi A, et al. 2021 December 10 

(opens in a new window)Network pharmacology: curing causal mechanisms instead of treating symptoms. Schmidt H et al. Trends in Pharmacological Sciences. 2021 December 9

(opens in a new window)Effects of Curcumin Analogues DMC and EF24 in Combination with the Cytokine TRAIL against Kidney Cancer. McMorrow T et al. Molecules. 2021 October 18

(opens in a new window)Autosomal dominant Shwachman-Diamond syndrome with a novel heterozygous missense variant in the SRP54 gene causing severe phenotypic features. Smith O et al. British Journal of Haematology. 2021 September 22

(opens in a new window)Immunological assessment of SARS-CoV-2 infection in pregnancy from diagnosis to delivery: A multicentre prospective study. Brennan D et al. PLOS One. 2021 September 20

(opens in a new window)Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines. Ryan CJ et al. Cell Systems. 2021 September 15

(opens in a new window)Personalised Medicine for Colorectal Cancer Using Mechanism-Based Machine Learning Models. Nwaokorie A, Fey D. International Journal of Molecular Sciences. 2021 September 15

(opens in a new window)Cell Adhesion Molecules in Normal Skin and Melanoma. Cian D'Arcy, Christina Kiel. Biomolecules. 2021 August 15

(opens in a new window)KBoost: a new method to infer gene regulatory networks from gene expression data. Kolch W et al. Scientific Reports. 2021 July 29

(opens in a new window)Engineering of Biological Pathways: Complex Formation and Signal Transduction. Junk P, Kiel C. Computational Design of Membrane Proteins. 2021 July 25

(opens in a new window)Modeling the Nonlinear Dynamics of Intracellular Signaling Networks. Rukhlenko OS, Kholodenko BN. Bio-Protocol. 2021 July 20

(opens in a new window)Channeling macrophage polarization by rocaglates increases macrophage resistance to Mycobacterium tuberculosis. Kramnik I et al. iScience. 2021 July 10

(opens in a new window)Reengineering protein-phosphorylation switches. Kholodenko, BN and Okada M. Science. 2021 July 02

(opens in a new window)Modeling Cervical Cancer Screening Strategies With Varying Levels of Human Papillomavirus Vaccination. Brennan D et al. JAMA Network Open. 2021 June 30

(opens in a new window)Nonvalvular atrial fibrillation patients anticoagulated with rivaroxaban compared with warfarin exhibit reduced circulating extracellular vesicles with attenuated pro-inflammatory protein signatures. Maguire P et al. Journal of Thrombosis and Haemostasis. 2021 June 23

(opens in a new window)A systematic analysis of signaling reactivation and drug resistance. Rukhlenko O et al. Cell Reports. 2021 May 25

(opens in a new window)Immature acute leukaemias: lessons from the haematopoietic roadmap. Bond J et al. The FEBS Journal. 2021 May 24

(opens in a new window)Detection and quanititation of host cell proteins in monoclonal antibody drug products using automated sample perparation and data-independent acquisition LC-MS/MS.Bones J et al. Journal of Pharmaceutical Analysis. 2021 May 20

(opens in a new window)Comparing 3D models of placenta accreta spectrum to surgical findings. Brennan D et al. International Journal of Gynaecology and Obstetrics. 2021 May 17 

(opens in a new window)Personalized Medicine for Neuroblastoma: Moving from Static Genotypes to Dynamic Simulations of Drug Response. Croucher D et al. MDPI: Journal of Personalised Medicine. 2021 May 11

(opens in a new window)A Chemo-Genomic Approach Identifies Diverse Epigenetic Therapeutic Vulnerabilities in MYCN-Amplified Neuroblastoma. Duffy D et al. Frontiers in Cell and Developmental Biology. 2021 April 21

(opens in a new window)Proteomic signatures of radioresistance: Alteration of inflammation, angiogenesis and metabolism-related factors in radioresistant oesophageal adenocarcinoma.Marcone S et al.Cancer Treatment and Research Communications.2021 April 18

(opens in a new window)Von Willebrand Factor, Factor VIII, and other acute phase reactants as biomarkers of inflammation and endothelial dysfunction in chronic Graft-versus-Host Disease. Lelas A et al.Frontiers in Immunology.2021 April 12

(opens in a new window)Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling. Nolan A et al.Genes.2021 April 10

(opens in a new window)Signaling pathways in intestinal homeostasis and colorectal cancer: KRAS at centre stage. Ternet C and Kiel C.Cell Communication and Signaling.2021 March 10

(opens in a new window)Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells. Parkhitko AA et al.PLoS Genetics.2021 Feb 17

(opens in a new window)IQGAP1 Is a Scaffold of the Core Proteins of the Hippo Pathway and Negatively Regulates the Pro-Apoptotic Signal Mediated by This Pathway. Quinn N et al.Cells.2021 Feb 13

(opens in a new window)Predicted 'wiring landscape' of Ras-effector interactions in 29 human tissues. Catozzi S et al.NPJ Systems Biology and Applications.2021 Feb 12

(opens in a new window)BAX and SMAC regulate bistable properties of the apoptotic caspase system. McKenna S et al.Scientific Reports.2021 Feb 8

(opens in a new window)The Ins and Outs of RAS Effector Complexes. Kiel C et al.Biomolecules. 2021 Feb 7

(opens in a new window)Mid-luteal uterine artery Doppler indices in the prediction of pregnancy outcome in nulliparous women undergoing assisted reproduction.Crosby DA et al.Human Fertility. 2021 Jan 13

(opens in a new window)Signaling Dynamics Regulating Crosstalks between T-Cell Activation and Immune Checkpoints. Kreileder M et al.Trends in Cell Biology.2020 Dec 30

(opens in a new window)Inhaled multi-walled carbon nanotubes differently modulate global gene and protein expression in rat lungs. Seidel C et al.Nanotoxicology. 2020 Dec 17

(opens in a new window)Perinatal Derivatives: Where Do We Stand? A Roadmap of the Human Placenta and Consensus for Tissue and Cell Nomenclature. Silini AR et al.Frontiers in Bioengineering and Biotechnology.2020 Dec 17

(opens in a new window)N-Linked glycosylation profiles of therapeutic induced senescent (TIS) triple negative breast cancer cells (TNBC) and their extracellular vesicle (EV) progeny. Kavanagh EL et al.Molecular omics.2020 Dec 16

(opens in a new window)Examination and characterisation of the effect of amitriptyline therapy for chronic neuropathic pain on neuropeptide and proteomic constituents of human cerebrospinal fluid. Royds J et al.Brain, Behavior, & Immunity - Health.2020 Dec 7

(opens in a new window)Accurate prediction of kinase-substrate networkds using knowledge graphs. Novacek V et al.PLoS Computational Biology. 2020 Dec 3

(opens in a new window)An Investigation into Proteomic Constituents of Cerebrospinal Fluid in Patients with Chronic Peripheral Neuropathic Pain Medicated with Opioids- a Pilot Study. Royds J et al.Journal of Neuroimmune Pharmacology.2020 Nov 20

(opens in a new window)SnapShot: APC/T Cell Immune Checkpoints. Shrager S and Kiel C.Cell. 2020 Nov 12

(opens in a new window)Improving response to progestin treatment of low-grade endometrial cancer. Baxter E at al.International Journal of Gynecological Cancer.2020 Nov 1

(opens in a new window)Differential responses of murine alveolar macrophages to elongate mineral particles of asbestiform and non-asbestiform varieties: Cytotoxicity, cytokine secretion and transcriptional changes. Khaliullin TO et al.Toxicology & Applied Pharmacology.2020 Oct 24

(opens in a new window)Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing. Rukhlenko O et al.Current Opinion in Structural Biology.2020 October 23

(opens in a new window)Prediction of chronic inflammation for inhaled particles: the impact of material cycling and quarantining in the lung epithelium. Kokot H et al.Advanced Materials.2020 Oct 19

(opens in a new window)The Molecular Effects of a High Fat Diet on Endometrial Tumour Biology.Wilkinson M et al.Life (Basel). 2020 Sept 10

(opens in a new window)Resolving the Interactome of the Human Immune Regulator MACIR with Enhanced Membrane Protein Preparation and Affinity Proteomics. McGauran G et al.Proteomics.2020 Aug 31

(opens in a new window)Combining Gene-Disease Associations with Single-Cell Gene Expression Data Provides Anatomy-Specific Subnetworks in Age-Related Macular Degeneration. Luther PJ, Kiel C.Network and Systems Medicine.2020 Aug 3 

(opens in a new window)Applications of personalised signalling network models in precision oncology. Hastings JF et al.Pharmacology & Therapeutics.2020 Aug 1

(opens in a new window)Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration. Bolado-Carrancio A et al.eLife. 2020 July 24

(opens in a new window)Examination and characterisation of burst spinal cord stimulation on cerebrospinal fluid cellular and protein constituents in patient responders with chronic neuropathic pain - A Pilot Study. Royds J et al.Journal of Neuroimmunology.2020 July 15

(opens in a new window)A transcriptomic continuum of differentiation arrest identifies myeloid interface acute leukemias with poor prognosis. Bond J et al.Leukemia. 2020 July 13

(opens in a new window)Toxicity of TiO2 Nanoparticles: Validation of Alternative Models. Leroux MM et al.International Journal of Molecular Sciences.2020 July 9

(opens in a new window)Fertility-sparing treatment in early endometrial cancer: current state and future strategies. Obermair A et al.Obstetrics & Gynecology Science.2020 July 8

(opens in a new window)Characterization of the renal cortical transcriptome following Roux-en-Y gastric bypass surgery in experimental diabetic kidney disease. Nair M et al.BMJ Open Diabetes Research & Care.2020 July 1

(opens in a new window)Increased extracellular vesicles mediate inflammatory signalling in cystic fibrosis.Useckaite Z et al.Thorax. 2020 June 1

(opens in a new window)Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions.Lord CJ et al.eLife.2020 May 28

(opens in a new window)Adverse outcome pathways as a tool for the design of testing strategies to support the safety assessment of emerging advanced materials at the nanoscale.Halappanavar S et al.Particle and Fibre Toxicology.2020 May 25

(opens in a new window)Curcumin Sensitizes Kidney Cancer Cells to TRAIL-Induced Apoptosis via ROS Mediated Activation of JNK-CHOP Pathway and Upregulation of DR4. Obaidi I et al.Biology (Basel).2020 May 1

(opens in a new window)Demodex: A skin resident in Man and his best friend. Foley R et al.Journal of the European Academy of Dermatology and Venereology. 2020 April 15

(opens in a new window)Acute Phase Response as a Biological Mechanism‐of‐Action of (Nano)particle‐Induced Cardiovascular Disease.Hadrup N et al.Small.2020 March 29

(opens in a new window)The Impact of Sarcopenia and Low Muscle Attenuation on Overall Survival in Epithelial Ovarian Cancer: A Systematic Review and Meta-analysis. McSharry V et al.Gynecologic Oncology.2020 March 27

(opens in a new window)Genetic Deletion of Zebrafish Rab28 Causes Defective Outer Segment Shedding, but Not Retinal Degeneration. Carter S et al. Frontiers in Cell and Developmental Biology. 2020 March 17

(opens in a new window)Genes expression profiling of alveolar macrophages exposed to non-functionalized, anionic and cationic multi-walled carbon nanotubes shows three different mechanisms of toxicity. Nahle S et al. Journal of Nanobiotechnology. 2020 Feb 24

(opens in a new window)A Quantitative Genetic Interaction Map of HIV Infection. Krogan N et al. Molecular Cell. 2020 Feb 20

(opens in a new window)Analysis of Ras-effector interaction competition in large intestine and colorectal cancer context. Kiel C et al. Small GTPases. 2020 Feb 14

(opens in a new window)Mitogen-Activated Protein Kinase (MAPK) and Obesity-Related Cancer. Donohoe F et al.International Journal of Molecular Sciences. 2020 Feb 13

(opens in a new window)Targeting MAPK Signaling in Cancer: Mechanisms of Drug Resistance and Sensitivity. Kolch W et al. International Journal of Molecular Sciences (Special Issue: Targeting MAPK in Cancer). 2020 Feb 7

(opens in a new window)Patient perceptions and understanding of obesity related endometrial cancer. Brennan DJ et al. Gynecologic Oncology Reports. 2020 May (online 31 Jan 2020)

(opens in a new window)Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D. Kolch W. Nature Communications. 2020 Jan 24

(opens in a new window)RASSF1A Tumour Suppressor: Target the Network for Effective Cancer Therapy. Matallanas D et al. Cancers. 2020 January 17

(opens in a new window)CBFβ-SMMHC Affects Genome-wide Polycomb Repressive Complex 1 Activity in Acute Myeloid Leukemia. Cordonnier G et al.Cell Reports.2020 Jan 14

(opens in a new window)Repository of proposed pathways and protein-protein interaction networks in age-related macular degeneration. Pool FM et al.NPJ Aging and Mechanisms of Disease.2020 Jan 7

(opens in a new window)Pharmacologic inhibition of hypoxia inducible factor (HIF)-hydroxylases ameliorates allergic contact dermatitis.Manresa, M.C. et al. Allergy. 2019;74(4): 753‐766

(opens in a new window)The extracellular matrix as a key regulator of intracellular signalling networks.Hastings, J.F. et al. British journal of pharmacology. 2019; 176(1): 82-92

(opens in a new window)A feasibility study of a multimodal stimulation bioreactor for the conditioning of stem cell seeded cardiac patches via electrical impulses and pulsatile perfusion.Herrmann, F.E.M. et al. Bio-medical materials and engineering. 2019; 30(1): 37-48

(opens in a new window)Mapping connections in signaling networks with ambiguous modularity.Lill, D. et al. NPJ systems biology and applications. 2019; 5, 19

(opens in a new window)Platelet-Derived Microparticles From Obese Individuals: Characterization of Number, Size, Proteomics, and Crosstalk With Cancer and Endothelial Cells.Grande, R. et al. Frontiers in pharmacology. 2019; 10, 7

(opens in a new window)Molecular basis of distinct oestrogen responses in endometrial and breast cancerBaxter, E. et al. Endocr Relat Cancer. 2019; 26(1): 31-46

(opens in a new window)DNMT3A mutation is associated with increased age and adverse outcome in adult T-acute lymphoblastic leukemia.Bond J. et al. Haematologica. 2019; 104(8): 1617‐1625.

(opens in a new window)Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. Erickson, K.E. et al. PLOS Comutational Biology. 2019; 17;15(1)

(opens in a new window)Hydroxylase Inhibition Selectively Induces Cell Death in Monocytes. Crifo, B. et al. The Journal of Immunology. 2019; 204(8)

(opens in a new window)Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival.Oser, M.G. et al. Cancer discovery. 2019; 9(2)

(opens in a new window)New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling. Erickson, K.E. et al. Seminars in Cancer biology. 2019; 54: 162-173

(opens in a new window)Understanding the role of distance, direction and cue salience in an associative model of landmark learning.Commins, S. & Fey, D. Scientific reports. 2019; 9(1), 2026

(opens in a new window)CBFβ-MYH11 interferes with megakaryocyte differentiation via modulating a gene program that includes GATA2 and KLF1.Yi, G. et al. Blood cancer journal.  2019; 9(3): 33

(opens in a new window)An Integrated Global Analysis of Compartmentalized HRAS Signaling.Santra, T. et al. Cell reports. 2019; 26(11): 3100‐3115

(opens in a new window)Targeting promiscuous heterodimerization overcomes innate resistance to ERBB2 dimerization inhibitors in breast cancer.Kennedy, S.P. et al. Breast Cancer Research. 2019; 21(1): 43

(opens in a new window)Evaluation of Demodex mite viability using motility and scattered light intensityGatault, S. et al. Experimental and Applied Acarology. 2019; 77: 463-469

(opens in a new window)Protein Hydroxylation by Hypoxia-Inducible Factor (HIF) Hydroxylases: Unique or Ubiquitous? Moritz, J. et al. Cells. 2019; 8(5): 384

(opens in a new window)All over the place: deciphering HRAS signaling from different subcellular compartmentsKolch, K. & Matallanas, D. Molecular & Cellular Oncology. 2019; 6(5): e1605821

(opens in a new window)Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation.Charitou, T. et al. British journal of cancer. 2019; 121(1): 37‐50

(opens in a new window)An integrative computational approach for a prioritization of key transcription regulators associated with nanomaterial-induced toxicity.Zhernovkov, V. et al. Toxicological sciences : an official journal of the Society of Toxicology. 2019; Online Preprint:kfz151

(opens in a new window)VGLL3 operates via TEAD1, TEAD3 and TEAD4 to influence myogenesis in skeletal muscle.Figeac N. et al. Journal of cell science. 2019; 132(13): jcs225946

(opens in a new window)Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry.Bouchal, P. et al. Cell reports. 2019; 28(3): 832-843

(opens in a new window)Hypoxia-inducible factor (HIF) hydroxylase inhibition enhances the protective effects of cyclosporine in colitis. Taylor, C.T. et al. American Journal of Physiology, Gastrointestinal and Liver Physiology. 2019; 317(2): G99-G97

(opens in a new window)Paralog buffering contributes to the variable essentiality of genes in cancer cell lines.De Kegel, B. & Ryan, C.J. PLoS genetics. 2019; 15(10): e1008466

(opens in a new window)Neutrophil gelatinase-associated lipocalin (NGAL) is localised to the primary cilium in renal tubular epithelial cells - A novel source of urinary biomarkers of renal injury.Cassidy, H. et al. Biochimica et biophysica acta. Molecular basis of disease. 2019; 1865(12): 165532

(opens in a new window)Mechanisms and consequences of oxygen-and carbon dioxide-sensing in mammals. Cummins, E.P. et al. Physiological Reviews. 2020; 100(1): 463‐488

(opens in a new window)Loss of RAF kinase inhibitor protein is involved in myelomonocytic differentiation and aggravates RAS-driven myeloid leukemogenesis.Caraffini, V. et al. Haematologica. 2020; 105(2): 375‐386

(opens in a new window)Epigenetics of paediatric acute myeloid leukaemia.Jones, L., McCarthy, P. & Bond, J. British journal of haematology. 2020; 188(1): 63‐76

(opens in a new window)Prolyl Hydroxylase Inhibition Mitigates PouchitisHarnoss, J.M. et al. Inflamatory Bowel Disease. 2020; 26(2): 192‐205

(opens in a new window)Protein and lipid homeostasis altered in rat macrophages after exposure to metallic oxide nanoparticles.Zahra, D. et al. Cell biology and toxicology. 2020;36(1):65‐82

(opens in a new window)Hypoxia in the GutTaylor, C.T.. Cellular and Molecular Gastroenterology and Hepatology. 2017; 5(1): 61-62

(opens in a new window)Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer.Ebhardt H.A. et al. NPJ Systems Biology and Applications. 2018; 4: 26

(opens in a new window)Sea turtle fibropapilloma tumors share genomic drivers and therapeutic vulnerabilities with human cancers.Duffy D.J. et al. Communications Biology. 2018; 1: 63

(opens in a new window)Increased Virulence of Bloodstream Over Peripheral Isolates of P. aeruginosa Identified Through Post-transcriptional Regulation of Virulence Factors.Hickey, C. et al. Frontiers in Cellular and Infection Microbiology. 2018; 8: 357

(opens in a new window)Acquisition of temporal HIF transcriptional activity using a secreted luciferase assayCavadas, M.A.S, Taylor, C.T. & Cheong, A.. Methods in Molecular Biology. 2018; 1742: 37‐44

(opens in a new window)Characterisation of HRas local signal transduction networks using engineered site-specific exchange factorsHerrero, A. et al. Small GTPases. 2017; 1‐13

(opens in a new window)Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line PanelsCampbell, J., Ryan, C.J. & Lord, C.J.. Methods in Molecular Biology. 2018;1711:83‐99

(opens in a new window)Integration of Omics Approaches and Systems Biology for Clinical Applications (Chapter 13. Introduction into the Concept of Systems Medicine)Vlahou, A. et al. John Wiley & Sons, Inc. DOI:10.1002/9781119183952

(opens in a new window)RASSF1A uncouples Wnt from Hippo signalling and promotes YAP mediated differentiation via p73.Papaspyropoulos, A. et al. Nature communications. 2018; 9(424)

(opens in a new window)ER and PR expression and survival after endometrial cancerSmith, D. et al. Gynecologic Oncology. 2018;148(2):258‐266

(opens in a new window)High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe.Roguev, A. et al. Cold Spring Harbor Protocols. 2018;2018(2):10.1101

(opens in a new window)Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for YeastRoguev, A. et al. Cold Spring Harbor Protocols. 2018;2018(2):10.1101

(opens in a new window)Metabolic stress regulates ERK activity by controlling KSR-RAF heterodimerization.Verlande, A. et al. EMBO reports. 2018;19(2):320‐336

(opens in a new window)FIGO consensus guidelines on placenta accreta spectrum disorders: IntroductionJauniaux, E. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 261-264

(opens in a new window)FIGO consensus guidelines on placenta accreta spectrum disorders: Prenatal diagnosis and screeningJauniaux, E. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 274-280

(opens in a new window)FIGO consensus guidelines on placenta accreta spectrum disorders: Nonconservative managementAllen, L. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 281-290

(opens in a new window)FIGO consensus guidelines on placenta accreta spectrum disorders: Conservative managementSentilhes, L. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 291-298

(opens in a new window)FIGO consensus guidelines on placenta accreta spectrum disorders: EpidemiologyJauniaux, E. et al. International Journal of Gynecology and Obstetrics. 2018; 140(3): 265-273

(opens in a new window)Transcriptionally inducible Pleckstrin homology-like domain, family A, member 1, attenuates ErbB receptor activity by inhibiting receptor oligomerizationMagi, S. et al. Journal of Biological Chemistry. 2018;293(6):2206‐2218

(opens in a new window)The PHD1 oxygen sensor in health and diseaseKennel, K.B. et al. The Journal of Physiology. 2018;596(17):3899‐3913

(opens in a new window)Identification of fungi in shotgun metagenomics datasetsDonovan, P.D. et al. PLoS ONE. 2018; 13 (2)

(opens in a new window)Novel Intergenically Spliced Chimera, NFATC3-PLA2G15, Is Associated with Aggressive T-ALL Biology and Outcome.Bond, J. et al. Molecular Cancer Research. 2018; 16(3): 470-475

(opens in a new window)New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signalingErickson, K.E. et al. Seminars in Cancer Biology. 2018; 54:162-173

(opens in a new window)The Birth and Death of Olfactory Receptor Gene Families in Mammalian Niche AdaptationHughes, G.M. et al. Mol Biol Evol. 2018; 35(6):139-1406

(opens in a new window)BAG3 promotes tumour cell proliferation by regulating EGFR signal transduction pathways in triple negative breast cancer.Shields, S. et al. Oncotarget. 2018; 9(21):15673-15690

(opens in a new window)E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer.Bajrami, I. et al. Cancer discovery. 2018; 8(4): 498-515

(opens in a new window)Enhancing Understanding of the Visual Cycle by Applying CRISPR/Cas9 Gene Editing in ZebrafishWard, R. et al. Frontiers Media. 2018; 6(37)

(opens in a new window)Early thymic precursor-like lymphomatous presentation of the ETV6-NCOA2 translocation.Bond, J. et al. British journal of haematology. 2018; 181(3): 392-394

(opens in a new window)Risk-adapted treatment of acute promyelocytic leukemia: results from International Consortium for Childhood APLTesti, A.M. et al. Blood. 2018; 132(4)

(opens in a new window)TPP riboswitch-dependent regulation of an ancient thiamin transporter in CandidaDonovan, P.D. et al. PLoS Genetics . 2018; 14(5)

(opens in a new window)Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer.Brough, R. et al. Oncogene. 2018; 37:5701-5718

(opens in a new window)Polycomb repressive complex 2 haploinsufficiency identifies a high-risk subgroup of pediatric acute myeloid leukemia.Bond, J. et al. Leukemia. 2018; 32(8): 1878-1882

(opens in a new window)Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle.Johnston, D. et al. Theriogenology. 2018; 114: 301-307

(opens in a new window)Identification of a MYCN and Wnt-related VANGL2-ITLN1 fusion gene in neuroblastomaDuffy D.J. et al. Gene Reports. 2018; 12: 187-200

(opens in a new window)Outcome of haematopoietic stem cell transplantation in dyskeratosis congenitaFioredda, F. et al. British Journal of Haematology. 2018; 183(1): 110-118

(opens in a new window)Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAnessHolme, H. et al. Scientific Reports. 2018; 8(1)

(opens in a new window)ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation.Monypenny, J. et al. Cell reports. 2018; 24(3): 630-641

(opens in a new window)PHD3 Regulates p53 Protein Stability by Hydroxylating Proline 359.Rodriguez, J. et al. Cell reports. 2018; 24(5): 1316-1329

(opens in a new window)Hypoxia‐sensitive pathways in intestinal inflammationBrown, E. & Taylor, C.T.. The Journal of Physiology. 2018: 596(15): 2985–2989

(opens in a new window)MASTL overexpression promotes chromosome instability and metastasis in breast cancer.Rogers, S. et al. Oncogene. 2018; 37(33): 4518-4533

(opens in a new window)Nanoparticles Can Wrap Epithelial Cell Membranes and Relocate Them Across the Epithelial Cell Layer.Urbančič, I. et al. Nano letters. 2018; 18(8): 5294-5305

(opens in a new window)Systems level expression correlation of Ras GTPase regulators.Besray Unal, E. et al. Cell Communication and Signaling. 2018; 16(1): 46

(opens in a new window)Author Correction: Chemosensitivity profiling of osteosarcoma tumour cell lines identifies a model of BRCAness.Holme, H. et al. Scientific Reports volume . 2018; 8(1)

(opens in a new window)Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling.Rukhlenko, O.S. et al. Cell systems. 2018; 7(2): 161-179

(opens in a new window)From oncogenic mutation to dynamic code.Kolch, W. & Kiel, C.. Science. 2018; 361(6405): 44-845

(opens in a new window)Gut adaptation after metabolic surgery and its influences on the brain, liver and cancerSinclair, P., Brennan, D.J. & le Roux, C.W.. Nature Reviews Gastroenterology & Hepatology. 2018; 15(10): 606–624

(opens in a new window)Synthetic Lethality and Cancer - Penetrance as the Major BarrierRyan, C.J., Bajrami, I. & Lord, C.J.. Trends Cancer. 2018; 4(10): 671-683

(opens in a new window)Systems biology: old news or new stimulus for biochemistry.Kolch, W., Fey, D. & Ryan, C.J.. Essays in biochemistry. 2018; 62(4): 483-486

(opens in a new window)Structure-based assessment and network analysis of targeting 14-3-3 proteins in prostate cancer.Root, A., Beizaei, A. & Ebhardt, H.A.. Molecular cancer. 2018; 17: 156

(opens in a new window)A two-drug combination simulation study for metastatic castrate resistant prostate cancer.Root, A. & Ebhardt, H.A.. The Prostate. 1196-1200

(opens in a new window)Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction.Thomaseth, C. et al. Scientific reports. 2018; 8, 16217

(opens in a new window)VarQ: A Tool for the Structural and Functional Analysis of Human Protein VariantsRadusky, L. et al. Front. Genet.. 2018; 9: 620

(opens in a new window)Quantitative Biology Theory, Computational Methods, and ModelsMunsky, B. et al. The MIT Press. ISBN: 9780262038089

(opens in a new window)Opportunities and Challenges of Whole-Cell and -Tissue Simulations of the Outer Retina in Health and DiseaseLuthert, P.J., Serrano, L. & Kiel, C.. Annual Review of Biomedical Data Science. 2018; 1: 131-152131-152

(opens in a new window)Association of Implementing a Multidisciplinary Team Approach in the Management of Morbidly Adherent Placenta With Maternal Morbidity and MortalityBartels, H. et al. Obstetrics & Gynecology. 2018; 132(5): 1167–1176

(opens in a new window)Reconstructing static and dynamic models of signaling pathways using Modular Response AnalysisSantra, T. et al. Current Opinion in Systems Biology. 2018; 9: 11-21

(opens in a new window)Clustal Omega for making accurate alignments of many protein sequencesSievers, F. & Higgins, D.G.. Protein Science. 2018; 27(1): 135–145

(opens in a new window)Improving machine learning in early drug discovery.Bendtsen, C. et al. Annals of Mathematics and Artificial Intelligence. 2017; 81,155-166.

(opens in a new window)Comprehensive proteome analysis of human skeletal muscle in cachexia and sarcopenia: a pilot study.Ebhardt, H.A. et al. Journal of Cachexia, Sarcopenia and Muscle. 2017; 8(4): 567–582.

(opens in a new window)The histone variant H2A. Z promotes splicing of weak introns.Kelly, E. et al. Genes & Development. 2017; 1;31(7): 688-701

(opens in a new window)CancerGD: A Resource for Identifying and Interpreting Genetic Dependencies in Cancer.Bridgett, S. Cell Systems. 2017; 26;5(1): 82-86.e3

(opens in a new window)Common and Distinctive Functions of the Hippo Effectors Taz and Yap in Skeletal Muscle Stem Cell Function.Sun, C. Stem Cells. 2017; 35(8): 1958–1972.

(opens in a new window)Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance.Duffy, D.J. et al Genome Medicine. 2017; 9: 15.

(opens in a new window)Lapatinib potentiates cytotoxicity of YM155 in neuroblastoma via inhibition of the ABCB1 efflux transporter.Radic-Sarikas, B. et al Scientific Reports. 2017; 7: 3091.

(opens in a new window)Hypoxia Reduces the Pathogenicity of Pseudomonas aeruginosa by Decreasing the Expression of Multiple Virulence Factors.Schaible, B. et al J Infect Dis. 2017; 1;215(9): 1459-1467

(opens in a new window)Protein multiple sequence alignment benchmarking through secondary structure prediction.Le, Q., Sievers, F. & Higgins, D.G. Bioinformatics. 2017; 1;33(9):1331-1337

(opens in a new window)Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models.Santra, T. et al PLOS ONE. 2017; 8;12(5):e0177058

(opens in a new window)Proteomics analysis of bladder cancer invasion: Targeting EIF3D for therapeutic intervention.Latosinska, A. et al Oncotarget. 2017; 19; 8(41): 69435–69455

(opens in a new window)A novel RNA sequencing data analysis method for cell line authentication.Fasterius, E. et al PLoS ONE. 2017; 13;12(2): e0171435

(opens in a new window)Vascular Endothelial Growth Factor (VEGF) Promotes Assembly of the p130Cas Interactome to Drive Endothelial Chemotactic Signalling and Angiogenesis.Evans, I.M. et al Mol Cell Proteomics. 2017; 16(2): 168-180.

(opens in a new window)Nambu bracket formulation of nonlinear biochemical reactions beyond mass action kinetics.Frank, T.D. Journal of Nonlinear Mathematical Physics. 2017; 19(1): 81-97.

(opens in a new window)Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models.Santra, T. et al PLOS one. 2017; 8;12(5): e0177058

(opens in a new window)A Bayesian non-parametric method for clustering high-dimensional binary data.Santra, T. Arxiv, 2017; 1603.02494

(opens in a new window)A Brain-Derived Neurotrophic Factor Mimetic Is Sufficient to Restore Cone Photoreceptor Visual Function in an Inherited Blindness Model.Daly, C. Scientific Reports. 2017; 12;7(1):11320

(opens in a new window)Performance of objective functions and optimisation procedures for parameter estimation in system biology models.Degasperi, A., Fey, D., Kholodenko, B.N. NPJ Systems Biology and Applications. 2017; 3: 20.

(opens in a new window)High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe.Roguev, A. et al Cold Spring Harbour Protocols. 2018:2018(2): 10

(opens in a new window)Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast.Roguev, A. et al Cold Spring Harbour Protocols. 2018; 2018(2):10

(opens in a new window)Hypoxia Inducible Factor (HIF) Hydroxylases as Regulators of Intestinal Epithelial Barrier Function.Manresa, M.C. & Taylor, C.T. Cell Mol GastroenterolHepato. 2017; 20;3(3):303-315

(opens in a new window)Determinants of hypoxia inducible factor (HIF) activity in the intestinal mucosa.Fagundes, R.R. & Taylor, C.T. J Appl Physiol. 2017; 1;123(5):1328-1334

(opens in a new window)The regulation of transcriptional repression in hypoxia.Cavadas, M.A.S., Cheong, A. & Taylor, C.T. Exp Cell Res. 2017; 15;356(2):173-181

(opens in a new window)Spatial regulation of ARAF controls the MST2-Hippo pathway.Rauch, J. & Kolch, W. Small GTPases. 2019; 10(4):243-248.

(opens in a new window)Personalized Computational Models as Biomarkers.Kolch, W. & Fey, D. Journal of Personalised Medicine. 2017; 7(3), 9.

(opens in a new window)FIH regulates cellular metabolism through hydroxylation of the deubiquitinase OTUB1.Scholz, C.C. et al. PLOS Biology. 2016 Jan 11;14(1):e1002347

(opens in a new window)HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.Bryan, K. et al. Journal of proteome research. 2016 Jun 3;15(6):2072-9.

(opens in a new window)Differential localization of A-Raf regulates MST2-mediated apoptosis during epithelial differentiation.Cell Death and Differentiation. Rauch, J. et al. 2016 Aug;23(8):1283-95.

(opens in a new window)Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF.Baljuls, A. et al. Cellular Signalling. 2016 Oct;28(10):1451-62

(opens in a new window)Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signalling Pathways.Rodriguez, J. et al. CELL Reports. 2016 Mar 22;14(11):2745-60.

(opens in a new window)Understanding complexity in the HIF signalling pathway using systems biology and mathematical modelling.Zsolt, F., Taylor, C.T. & Nguyen, L.K. Journal of Molecular Medicine. 2016 Apr;94(4):377-90

(opens in a new window)Wnt6 regulates epithelial cell differentiation and is dysregulated in renal fibrosis.Beaton, H., et al. American Journal of Physiology. 2016 Jul 1;311(1):F35-45

(opens in a new window)Hypercapnia Suppresses the HIF-dependent Adaptive Response to Hypoxia.Selfridge, A.C. et al. The Journal of Biological Chemistry. 2016 May 27;291(22):11800-8.

(opens in a new window)The role of HIF in immunity and inflammation.Cummins, E.P. et al. Molecular Aspects of Medicine. Feb-Mar 2016;47-48:24-34.

(opens in a new window)Crosstalk between toll-like receptors and hypoxia-dependent pathways in health and disease.Crifo, B. & Taylor, C.T. Journal of Investigative Medicine. 2016 Feb;64(2):369-75.

(opens in a new window)Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines.Campbell, J. et al. Cell Reports. 2016 Mar 15;14(10):2490-501.

(opens in a new window)Bistability in the Rac1, PAK, and RhoA Signalling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches.Byrne, K.M. et al. Cell Systems. 2016 Jan 27;2(1):38-48.

(opens in a new window)PP1 initiates the dephosphorylation of MASTL, triggering mitotic exit and bistability in human cells.Rogers, S. et al. Journal of Cell Science. 2016 Apr 1;129(7):1340-54.

(opens in a new window)Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis.Rinaldi, L. et al. Cell Stem Cell. 2016 Oct 6;19(4):491-501.

(opens in a new window)Integrating network reconstruction with mechanistic modelling to predict cancer therapies.Halasz, M. et al. Science Signalling. 2016 Nov 22;9(455):ra114.

(opens in a new window)Bayesian algorithm for detecting differentially expressed proteins and its application in breast cancer research.Santra, T., Delatola, E.A. Scientific Reports. 2016 Jul 22;6:30159.

(opens in a new window)BGRMI: A method for inferring gene regulatory networks from time-course gene expression data and its application in breast cancer research.Iglesius Martinez, L.F., Kolch W., Santra, T. Scientific Reports. 2016 Nov 23;6:37140.

(opens in a new window)Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy.Zhang, R. et al. ACS Nano. 2017 Jan 24;11(1):249-257.

(opens in a new window)HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status.Weitsman, G. et al. Oncotarget. 2016 Aug 9;7(32):51012-51026.

(opens in a new window)Rac1 and RhoA: networks, loops and bistability.Nguyen, L.K., Kholodenko, B.N. & von Kriegsheim, A. Small GTPases. 2018 Jul 4;9(4):316-321.

(opens in a new window)Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data.Frank, T.D. et al. Mathematical Medicine and Biology. 2017 Jun 1;34(2):177-191

(opens in a new window)ATR inhibitors as a synthetic lethal therapy for tumours deficient in ARID1A.Williamson, C.T. et al. Nature Communications. 2016 Dec 13;7:13837.

(opens in a new window)Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF.Baljuls, A. et al. Cellular Signalling. 2016 Oct;28(10):1451-62.

(opens in a new window)Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease.Stanley, E. et al. BMC Bioinformatics. 2016 Dec 6;17(1):496.

(opens in a new window)SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.Sánchez-Sanz, G. et al. PLoS Comput Biol. 2016 Oct 7;12(10):e1005051.

(opens in a new window)REST is a hypoxia-responsive transcriptional repressor.Cavadas, M.A.S. et al. Scientific Reports. 2016 Aug 17;6:31355.

(opens in a new window)Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signalling Pathways.Rodriguez, J. et al. Cell Reports. 2016 Mar 22;14(11):2745-60.

(opens in a new window)Proteome-wide association studies identify biochemical modules associated with a wing size phenotype in Drosophila melanogaster.Okada H. et al. Nature Communications. 2016 Sep 1;7:12649.

(opens in a new window)Autophosphorylation on S614 inhibits the activity and the transforming potential of BRAF.Dernayka, L. et al. Cellular Signalling. 2016 Sep;28(9):1432-9.

(opens in a new window)Mesenchymal Stromal Cells Protect Endothelial Cells from Cytotoxic T Lymphocyte-Induced Lysis.Cahill, E.F. et al. Scandinavian Journal of Immunology. 2016 Sep;84(3):158-64.

(opens in a new window)Wnt signalling is a bi-directional vulnerability of cancer cells.Duffy, D.J. et al. Oncotarget. 2016 Sep 13;7(37):60310-60331.

(opens in a new window)MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance.Rauch, N. et al. Current Opinion in Structural Biology. 2016 Dec;41:151-158.

(opens in a new window)The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells.Fey, D. et al. Seminars in Cell and Developmental Biology. 2016 Oct;58:96-107.

(opens in a new window)The MST/Hippo pathway and cell death: A non-canonical affair.Fallahi, E., O'Driscoll, N.A. & Matallanas, D. Genes. 2016 Jun 17;7(6):28.

(opens in a new window)Hypoxia-dependent regulation of inflammatory pathways in immune cells.Taylor, C.T. et al. Journal of Clinical Investigation. 2016 Oct 3;126(10):3716-3724

(opens in a new window)VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis.Evans, I.M. et al, Molecular and Cellular Proteomics. 2017 Feb;16(2):168-180.

(opens in a new window)Regulation of the MAPK pathway by raf kinase inhibitory protein.Vandamme, D. et al. Critical Reviews in Oncogenesis, 2014;19(6):405-15.

(opens in a new window)Signalling mechanisms regulating phenotypic changes in breast cancer cells.Volinsky, N. et al. Biosci Rep,. 2015 Mar 18;35(2):e00178.

(opens in a new window)Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation.Milewska, M. et al. PLoS ONE, 2015 Jun 12;10(6):e0129859.

(opens in a new window)Competing to coordinate cell fate decisions: the MST2-Raf-1 signalling device.Nguyen, L.K. et al. Cell Cycle. 2015;14(2):189-99.

(opens in a new window)Mechanochemical stimulation of MCF7 cells with rod-shaped Fe-Au Janus particles induces cell death through paradoxical hyperactivation of ERK.Kilinc, D. et al. Advanced healthcare materials. 2015 Feb 18;4(3):395-404.

(opens in a new window)Advances in dynamic modelling of colorectal cancer signalling-network regions, a path toward targeted therapies.Tortolina, L. et al. Oncotarget. 2015 Mar 10;6(7):5041-58.

(opens in a new window)Network-based identification of feedback modules that control RhoA activity and cell migration.Kim, T.H. et al. Journal of Molecular Cell Biology. 2015 Jun;7(3):242-52.

(opens in a new window)ROCK activity and the Gβγ complex mediate chemotactic migration of mouse bone marrow-derived stromal cells.Ryan, C.M. et al. Stem Cell Research and Therapy. 2015 Jul 24;6:136.

(opens in a new window)The dynamic control of signal transduction networks in cancer cells.Kolch, W. et al. Nature Reviews Cancer. 2015 Sep;15(9):515-27.

(opens in a new window)Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification.Schwarzl, T. et al. Molecular Biology. 2015 Oct 23;427(21):3368-74.

(opens in a new window)Protein-protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose-responses.Varusai, T.M. et al. Molecular BioSystems. 2015 Oct;11(10):2750-62.

(opens in a new window)In vitro study of the interaction of heregulin-functionalized magnetic-optical nanorods with MCF7 and MDA-MB-231 cells.Lesniak, A. ety al. Faraday Discussions. 2014;175:189-201.

(opens in a new window)CrosstaL.K. between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function Cell Host Microbe.Kelly, C.J. et al. Cell Host Microbe, 2015 May 13;17(5):662-71.

(opens in a new window)Silence on the relevant literature and errors in implementation.Bastiaens, P. et al. Nature Biotechnology. 2015 Apr;33(4):336-9.

(opens in a new window)Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.Patrick, K.L. et al. PLOS Genetics. 2015 Mar 31;11(3):e1005074.

(opens in a new window)Species differential regulation of COX2 can be described by an NFkB-dependent logic AND gate Cellular and Molecular Life Sciences.Nguyen, L.K. et al. 2015 Jun;72(12):2431-43.

(opens in a new window)Paricalcitol protects against TGF1-induced fibrotic responses in hypoxia and stabilises HIF in renal epithelia.Nolan, K.A. et al. Exp Cell Res. 2015 Jan 15;330(2):371-81

(opens in a new window)Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity.Nagashima, T. et al. The FEBS Journal. 2015 Feb;282(4):613-29.

(opens in a new window)The impact of hypoxia on bacterial infection.Schaffer, K. & Taylor, C.T. FEBS Journal. 2015 Jun;282(12):2260-6.

(opens in a new window)A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) network.Nguyen, L.K. et al. Journal of Cell Science. 2015 Jan 15;128(2):422.

(opens in a new window)DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks.Nguyen, L.K. et al. Scientific Reports. 2015 Jul 29;5:12569.

(opens in a new window)Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects.Kholodenko, B.N. Cell Reports. 2015 Sep 22;12(11):1939-49.

(opens in a new window)Feedback regulation in cell signalling: Lessons for cancer therapeutics.Nguyen, L.K. & Kholodenko. B.N. Seminars in Cell and Developmental Biology. 2016 Feb;50:85-94.

(opens in a new window)MST2-RASSF protein-protein interactions through SARAH domains.Sanchez-Sanz, G. et al. Briefings in bioinformatics. 2016 Jul;17(4):593-602

(opens in a new window)Advances in dynamic modelling of colorectal cancer signalling-network regions, a path toward targeted therapies.Tortolina, L. et al. OncoTarget. 2015 Mar 10;6(7):5041-58.

(opens in a new window)p19-INK4d inhibits neuroblastoma cell growth, induces differentiation and is hypermethylated and downregulated in MYCN-amplified neuroblastomas.Dreidax, D. et al. Human Molecular Genetics. 2014 Dec 20;23(25):6826-37.

(opens in a new window)Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure.Guerriero, M.L., Ozgur, A.E. & van Ooijen, G. Frontiers in Plant Science. 2014 Oct 21;5:564.

(opens in a new window)Mechanochemical stimulation of MCF7 cells with rod-shaped Fe-Au Janus particles induces cell death through paradoxical hyperactivation of ERK.Kilinc, D. et al. Advanced Healthcare Materials. 2015 Feb 18;4(3):395-404.

(opens in a new window)Integrated signalling pathway and gene expression regulatory model to dissect dynamics of Escherichia coli challenged mammary epithelial cells. den Breems, N., Nguyen, L.K. & Kulasiri D. BioSystems. 2014 Dec;126:27-40.

(opens in a new window)Ubiquitin chain specific auto-ubiquitination triggers sustained oscillation, bistable switches and excitable firing.Nguyen, L.K. et al. IET Systems Biology. 2014 Dec;8(6):282-92.

(opens in a new window)HEATR2 Plays a Conserved Role in Assembly of the Ciliary Motile Apparatus.Diggle, C.P. et al. PloS Genet. 2014 Sep 18;10(9):e1004577.

(opens in a new window)Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses.Dobrzyński, M. et al. J. R. Soc. Interface. 2014 Sep 6;11(98):20140383.

(opens in a new window)One Hippo and many masters: differential regulation of the Hippo pathway in cancer.Romano, D. et al. Biochem Soc Trans. 2014 Aug;42(4):816-21.

(opens in a new window)Robustness and Evolvability of the Human Signalling Network.Junil, K., et al. PLOS Computational Biology. 2014 Jul 31;10(7):e1003763.

(opens in a new window)GSK3 Inhibitors Regulate MYCN mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms, Including p53 and Wnt Signalling.Duffy, D.J. et al. Mol Cancer Ther. 2014 Feb;13(2):454-67.

(opens in a new window)Primary cilium-associated genes mediate bone marrow stromal cell response to hypoxia.Brown, J.A.L. et al. Stem Cell Research. 2014 Sep;13(2):284-99.

(opens in a new window)Protein interaction switches coordinate Raf-1 and MST2/Hippo signalling.Romano, D. et al. Nature Cell Biology. 2014 Jul;16(7):673-84.

(opens in a new window)Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells.Jiwaji, M. et al. PLoS ONE. 2014 Jun 13;9(6):e99458.

(opens in a new window)Interplay of DNA damage and cell cycle signalling at the level of human replication protein A DNA Repair.Borgstahl, G.E.O. et al. 2014 Sep;21:12-23.

(opens in a new window)HGF Induces Epithelial-to-Mesenchymal Transition by Modulating the Mammalian Hippo/MST2 and ISG15 Pathways.Farrell, J. et al. Journal of Proteome Research. 2014 Jun 6;13(6):2874-86.

(opens in a new window)Illuzzi, G. et al. PARG is dispensable for recovery from transient replicative stress but required to prevent detrimental accumulation of poly (ADP-ribose) upon prolonged replicative stressNucleic Acids Research. 2014 Jul; 42(12):7776-92.

(opens in a new window)Investigation of the possible functions of PACAP in human trophoblast cells.Horvath, G. et al. J Mol Neurosci. 2014 Nov;54(3):320-30.

(opens in a new window)A Bayesian framework that integrates heterogeneous data for inferring gene regulatory networks.Santra, T. Frontiers in Bioengineering and Biotechnology. 2014 May 20;2:13

(opens in a new window)Interplay of DNA damage and cell cycle signalling at the level of human replication protein A DNA Repair.Borgstahl, G.E.O. et al. 2014 Sep;21:12-23.

(opens in a new window)Human adipocytes are highly sensitive to intermittent hypoxia induced NF-kappaB activity and subsequent inflammatory gene expression.Taylor, C.T. et al. Biochemical and Biophysical Research Communications. 2014 May 16;447(4):660-5.

(opens in a new window)Mig-6 participates in the regulation of cell senescence and retinoblastoma protein phosphorylation.Milewska, M. & Kolch, W. Cellular Signalling. 2014 Sep;26(9):1870-7.

(opens in a new window)On-Beads Digestion in Conjunction with Data-Dependent Mass Spectrometry: A Shortcut to Quantitative and Dynamic Interaction.Turriziani, B. et al. Proteomics Biology. 2014 Apr 16;3(2):320-32.

(opens in a new window)The APC network regulates the removal of mutated cells from colonic crypts.Song, J.H. et al. Cell Reports. 2014 Apr 10;7(1):94-103.

(opens in a new window)Basic fibroblast growth factor modifies the hypoxic response of human bone marrow stromal cells by ERK-mediated enhancement of HIF-1 activity.Fábián, Z. et al. Stem Cell Research.

(opens in a new window)Splicing factor hnRNP A2 activates the Ras-MAPK-ERK pathway by controlling A-Raf splicing in hepatocellular carcinoma developmentRNA. Shilo, S. et al. 2014 Apr; 20(4): 505–515.

(opens in a new window)Navigating the Multilayered Organization of Eukaryotic Signalling: A New Trend in Data Integration.Santra, T., Kolch, W. & Kholodenko, B.N. PLOS Computational Biology. 2014 Feb 13;10(2):e1003385.

(opens in a new window)Evaluating Strategies to Normalise Biological Replicates of Western Blot Data.Degasperi, A. et al. PLOS One. 2014 Jan 27;9(1):e87293.

(opens in a new window)Polyubiquitin chain assembly and organisation determine the dynamics of protein activation and degradation.Nguyen, L.N. et al. Frontiers in Physiology. 2014 Jan 24;5:4.

(opens in a new window)DAISY: picking synthetic lethals from cancer genomes.Ryan, C.J., Lord, C.J. & Ashworth A. Cancer Cell. 2014 Sep 8;26(3):306-308

(opens in a new window)Editorial: A PHD in macrophage survival J Leukoc Biol.Taylor, C.T. & Scholz, C.C. 2014 Sep;96(3):359-61.

(opens in a new window)Systems biology-embedded target validation: improving efficacy in drug discovery.Vandamme, D. et al. Wiley Interdiscip Rev Syst Biol Med. Jan-Feb 2014;6(1):1-11.

(opens in a new window)Allogeneic murine mesenchymal stem cells: migration to inflamed joints in vivo and amelioration of collagen induced arthritis when transduced to express CTLA4Ig.Sullivan, C. et al. Stem cells dev. 2013 Dec 15;22(24):3203-13.

(opens in a new window)Regulation of IL-1-induced NF-B by hydroxylases links key hypoxic and inflammatory signalling pathways.Scholz, C.C. et al. Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18490-5.

(opens in a new window)Tyr728 in the Kinase Domain of the Murine Kinase Suppressor of RAS 1 regulates Binding and Activation of the Mitogen-activated Protein Kinase Kinase.Sibilski, C. et al. J Biol Chem. 2013 Dec 6;288(49):35237-52.

(opens in a new window)Extracellular signal-regulated kinase regulates RhoA activation and tumor cell plasticity by inhibiting guanine exchange factor H1 activity.von Thun, A. et al. Mol Cell Biol. 2013 Nov;33(22):4526-37.

(opens in a new window)Cell cycle-dependent formation of Cdc45-Claspin complexes in human cells are compromised by UV-mediated DNA damage.Broderick, R. et al. FEBS Journal. 2013 Oct;280(19):4888-902.

(opens in a new window)RCP-driven α5β1 recycling suppresses Rac and promotes RhoA activity via the RacGAP1-IQGAP1 complex.Jacquemet, G. et al. J Cell Biol. 2013 Sep 16;202(6):917-35.

(opens in a new window)When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling.Nguyen, L.K., Kolch, W. & Kholodenko, B.N. Cell Communication and Signalling. 2013 Jul 31;11:52.

(opens in a new window)Control of the G-protein Cascade Dynamics by GDP Dissociation Inhibitors.Nikonova, E. et al. Molecular Biosystems. 2013 Oct;9(10):2454-62.

(opens in a new window)Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2.Reiterer, V. et al. Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):E2934-43.

(opens in a new window)Temporal regulation of EGF signalling networks by the scaffold protein Shc1.Zheng, Y. et al. Nature. 2013 Jul 11;499(7457):166-71.

(opens in a new window)Increased baseline proinflammatory cytokine production in chronic hepatitis C patients with rapid virological response to peginterferon plus ribavirin.Par, G.et al. PLOS One. 2013 Jul 9;8(7):e67770.

(opens in a new window)Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology.Santra, T. et al. BMC Systems Biology. 2013 Jul 6;7:57.

(opens in a new window)The Effect of Temperature Elevation on Cryopreserved Mesenchymal.Norkus, M. et al. Stem Cells Cryo Letters. Jul-Aug 2013;34(4):349-59.

(opens in a new window)Progesterone-Induced Blocking Factor differentially regulates trophoblast and tumour invasion by altering matrix metalloproteinase activity.Halasz, M. et al. Cell. Mol. Life Sci. 2013 Dec;70(23):4617-30.

(opens in a new window)Hippocampal contribution to vector model hypothesis during cue-dependent navigation.Diviney, M., Fey, D. & Commins, S. Learn Mem. 2013 Jun 17;20(7):367-78.

(opens in a new window)Growth differentiation factor-5 enhances in vitro mesenchymal stromal cell chondrogenesis and hypertrophy.Coleman, C.M. et al. Stem Cells Dev. 2013 Jul 1;22(13):1968-76.

(opens in a new window)Hypoxia-inducible factor (HIF) network: insights from mathematical models.Cavadas, M.A.S., Nguyen, L.N., & Cheong, A. Cell Communication and signalling. 2013 Jun 10;11(1):42. #

(opens in a new window)A Process Algebra Framework for Multi-Scale Modelling of Biological Systems.Degasperi, A. & Calder, M. Theoretical Computer Science. 2013 June;488(3):15-45.

(opens in a new window)Impact of Mesenchymal Stem Cell secreted PAI-1 on colon cancer cell migration and proliferation.Hogan, N.M. et al. Biochemical and Biophysical Research Communication. 2013 Jun 14;435(4):574-9.

(opens in a new window)Effects of intratracheal mesenchymal stromal cell therapy during recovery and resolution after ventilator-induced lung injury.Curley, G.F. et al. Anesthesiology. 2013 Apr;118(4):924-32.

(opens in a new window)Phosphodiesterase-8A binds to and regulates Raf-1 kinase.Brown, K.M. et al Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):E1533-42.

(opens in a new window)The differential effects of wild-type and mutated K-Ras on MST2 signalling are determined by K-Ras activation kinetics.Romano, D. et al. Mol Cell Biol. 2013 May;33(9):1859-68.

(opens in a new window)Liposomal surface coatings of metal stents for efficient non-viral gene delivery to the injured vasculature.Ganly, S. et al. Journal of Controlled Release. 2013 Apr 28;167(2):109-19.

(opens in a new window)A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network.Nguyen, L.K. et al. J Cell Sci. 2013 Mar 15;126(Pt 6):1454-63.

(opens in a new window)Involvement of Lyn and the Atypical Kinase SgK269/PEAK1 in a Basal Breast Cancer Signalling Pathway.David, R. et al. Cancer Research. 2013 Mar 15;73(6):1969-80.

(opens in a new window)Thermoresponsive substrates used for the expansion of human mesenchymal stem cells and the preservation of immunophenotype.Nash, M.E. et al. Stem Cell Rev. 2013 Apr;9(2):148-57.

(opens in a new window)Raf kinase inhibitor protein expression combined with peritoneal involvement and lymphovascular invasion predicts prognosis in Dukes' B colorectal cancer patients.Doyle, B. et al. Histopathology. 2013 Feb;62(3):505-10.

(opens in a new window)A limit cycle oscillator model for cycling mood variations of bipolar disorder patients derived from cellular biochemical reaction equations.Frank, T.D. Communications in Nonlinear Science and Numerical Simulation. 2013 Aug;18(8):2107-2119

(opens in a new window)Systems medicine: opportunities and challenges for systems biology approaches.Kolch, W. & Kholodenko, B.N. FEBS journal. 2013 Dec;280(23):5937.

(opens in a new window)Mesenchymal stem cells in joint disease and repair.Barry, F. & Murphy, M. Nature Reviews Rheumatology. 2013 Oct;9(10):584-94.

(opens in a new window)Carbon dioxide-sensing in organisms and its implications for human disease.Cummins, E.P. et al. Cell Mol Life Sci. 2014 Mar;71(5):831-45.

(opens in a new window)Organizing a PhD symposium: an inside view.Schröder, M.S. et al. EMBO reports. 2013 Oct;14(10):856-60.

(opens in a new window)Complexity of receptor tyrosine kinase signal processing.Volinsky, N., Kholodenko, B.N. Cold Spring Harbor Perspectives in Biology. 2013 Aug 1;5(8):a009043.

(opens in a new window)Systems medicine: helping us understand the complexity of disease.Vandamme, D. et al. QJM. 2013 Oct;106(10):891-5.

(opens in a new window)Targeting the HIF pathway in inflammation and immunity.Scholz, C.C. & Taylor, C.T. Curr Opin Pharmacol. 2013 Aug;13(4):646-53.

(opens in a new window)Hydroxylase-dependent regulation of the NF-κB pathway.Scholz, C.C. & Taylor, C.T. Biol Chem. 2013 Apr;394(4):479-93.

(opens in a new window)Big Signals from Small Particles: Regulation of Cell Signalling Pathways by Nanoparticles.Rauch, J. et al. Chemical Reviews. 2013 May 8;113(5):3391-406

(opens in a new window)The role of progesterone in implantation and trophoblast invasion.Halasz, M. & Szekeres-Bartho, J. J Reprod Immunol. 2013 Mar;97(1):43-50.

(opens in a new window)Monitoring of Transcriptional Dynamics of HIF and NF-κB.Cavadas, M. & Cheong, A. Methods Mol. Biol. 2014;1098:97-105.

(opens in a new window)Encyclopedia of Signalling Molecules: A-Raf kinase.Rauch, J. & Kolch, W. Encyclopedia of Signalling Molecules. ISBN:978-1-4614-6438-9

(opens in a new window)Physiological Temperature Has a Crucial Role in Amyloid Beta in the Absence and Presence of Hydrophobic and Hydrophilic Nanoparticles.Ghavami, M. et al. ACS Chem. Neurosci. 2013 Mar 20;4(3):375-8.

(opens in a new window)Unique Reporter-Based Sensor Platforms to Monitor Signalling in Cells.Jiwaji, M. et al. PLOS One. 2012;7(11):e50521.

(opens in a new window)High levels of ephrinB2 over-expression increases the osteogenic differentiation of human mesenchymal stem cells and promotes enhanced cell mediated mineralisation in a polyethyleneimine-ephrinB2 gene-activated matrix.Tierney, E.G. et al. Journal of Controlled Release. 2013 Feb 10;165(3):173-82.

(opens in a new window)Mitochondrial reactive oxygen species enhance AMPK activation in the endothelium of patients with coronary artery disease and diabetes.Mackenzie, R.M. et al. Clinical Science. 2013 Mar;124(6):403-11.

(opens in a new window)Cell Type-Specific Activation of AKT and ERK Signalling Pathways by Small Negatively-Charged Magnetic Nanoparticles.Rauch, J., Kolch, W. & Mahmoudi, M. Sci. Rep. 2012;2:868.

(opens in a new window)Doxorubicin induces the DNA damage response in cultured human mesenchymal stem cells.Cruet-Hennequart, S. et al. Int J Hematol. 2012 Nov;96(5):649-56.

(opens in a new window)Predictors of quality of life gains among people with type 1 diabetes participating in the Dose Adjustment for Normal Eating (DAFNE) structured education programme.Byrne, M. et al. Diabetes Res Clin Pract. 2012 Nov;98(2):243-8.

(opens in a new window)Crosstalk and signalling switches in mitogen-activated protein kinase cascades.Fey, D. et al. Frontiers in Physiology. 2012 Sep 18;3:355.

(opens in a new window)Mammalian Protein Expression Noise: Scaling Principles and the Implications for Knockdown Experiments.Birtwistle, M.R. et al. Mol. BioSyst. 2012 Nov;8(11):3068-76.

(opens in a new window)Isolation and Phenotypic Characterisation of Stem Cells from late Stage Osteoarthritic Mesenchymal Tissues.Labusca, L. et al. Curr Stem Cell Res Ther. 2012 Sep;7(5):319-28.

(opens in a new window)Imatinib-dependent tyrosine phosphorylation profiling of Bcr-Abl-positive chronic myeloid leukemia cells.Preisinger, C. et al. Leukemia. 2013 Mar;27(3):743-6.

(opens in a new window)Emergence of bimodal cell population responses from the interplay between analog single-cell signalling and protein expression noise.Birtwistle, M.R. et al. BMC Syst Biol. 2012 Aug 24;6:109.

(opens in a new window)Segregation of Replicative DNA Polymerases during S Phase: DNA Polymerase epsilon but not DNA Polymerases alpha/delta, are associated with lamins throughout the S phase in human cells.Vaara, M. et al. J Biol Chem. 2012 Sep 28;287(40):33327-38.

(opens in a new window)Cells lacking β-actin are genetically reprogrammed and maintain conditional migratory capacity.Tondeleir, D. et al. Molecular & Cellular Proteomics. 2012 Aug;11(8):255-71.

(opens in a new window)The electrical stimulation of carbon nanotubes to provide a cardiomimetic cue to MSCs.Mooney, E. et al. Biomaterials. 2012 Sep;33(26):6132-9.

(opens in a new window)A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction.Watterson, S. et al. Biochimie. 2013 Mar;95(3):613-21.

(opens in a new window)Establishment and initial characterization of SOX2-overexpressing NT2/D1 cell clones.Drakulic, D., Krstic, A. & Stevanovic, M. Genetics and Molecular Research. 2012 May 15;11(2):1385-400.

(opens in a new window)Kinetics of thermally induced heat shock protein 27 and 70 expression by bone marrow-derived mesenchymal stem cells.Moloney, T.C. et al. Protein Sci. 2012 Jun;21(6):904-9.

(opens in a new window)On the application of active learning and gaussian processes in postcryopreservation cell membrane integrity experiments.Norkus, M. et al. IEEE/ACM Trans Comput Biol Bioinform. May-Jun 2012;9(3):846-56.

(opens in a new window)Development of a thermoresponsive chitosan gel combined with human mesenchymal stem cells and desferrioxamine as a multimodal pro-angiogenic therapeutic for the treatment of critical limb ischaemia.Hastings, C.L. et al. J Control Release. 2012 Jul 10;161(1):73-80.

(opens in a new window)The role of modern imaging techniques in the diagnosis of malposition of the branch pulmonary arteries and possible association with microdeletion 22q11.2.Cuturilo, G. et al. Cardiology in the Young. 2013 Apr;23(2):181-8.

(opens in a new window)Hypercapnia induces cleavage and nuclear localization of Rel B giving insight into CO2 sensing and signalling.Oliver, K.M. et al. J Biol Chem. 2012 Apr 20;287(17):14004-11.

(opens in a new window)Cell Cycle-Dependent Mobility of Cdc45 Determined in vivo by Fluorescence Correlation Spectroscopy.Broderick, R. et al. PLoS One. 2012 April; 7(4): e35537.

(opens in a new window)Versatility of cooperative transcriptional activation: a thermodynamical modelling analysis for greater-than-additive and less-than-additive effect.Frank, T.D., Carmody, A.M. & Kholodenko, B.N. PLoS One. 2012;7(4):e34439.

(opens in a new window)Catching transcriptional regulation by thermostatistical modelling.Frank, T.D. et al. Phys. Biol. 2012 Aug;9(4):045007.

(opens in a new window)Glucose reintroduction triggers the activation of Nrf2 during experimental ischemia reperfusion.Crean, D. et al. Mol Cell Biochem. 2012 Jul;366(1-2):231-8.

(opens in a new window)Regulation of oscillation dynamics in biochemical systems with dual negative feedback loops.Nguyen, L.K. J R Soc Interface. 2012 Aug 7;9(73):1998-2010.

(opens in a new window)Oscillatory nonequilibrium Nambu systems: the canonical-dissipative Yamaleev oscillator.Mongkolsakulvong, S., Chaikan, P. & Frank, T.D. European Physical Journal B. 2012 March; 85(90)

(opens in a new window)Hypercapnia induces cleavage and nuclear localization of RELB giving insight into CO2 sensing and signalling.Oliver, K.M. et al. J. Biol. Chem. 2012 Apr 20;287(17):14004-11.

(opens in a new window)Frequent loss of RAF kinase inhibitor protein expression in acute myeloid leukemia.Zebisch, A. et al. Leukemia. 2012 Aug;26(8):1842-9.

(opens in a new window)PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity.Tibarewal P. et al. Sci Signal. 2012 Feb 28;5(213):ra18.

(opens in a new window)ERK2 drives tumour cell migration in three-dimensional microenvironments by suppressing expression of Rab17 and liprin-β2.von Thun, A. et al. J Cell Sci. 2012 Mar 15;125(Pt 6):1465-77.

(opens in a new window)Pre-treatment of Endothelial Progenitor Cells with Osteopontin Enhances Cell Therapy for Peripheral Vascular Disease.Vaughan, E.E. et al. Cell Transplant. 2012;21(6):1095-107.

(opens in a new window)Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance.Aksamitiene, E., Kiyatkin, A. & Kholodenko, B.N. Biochemical Society Transactions. 2012 Feb;40(1):139-46.

(opens in a new window)Symmetry breaking analysis of prism adaptation's latent aftereffect.Frank, T.D., Blau, J.J.C. & Turvey, M.T. Cognitive Science. May-Jun 2012;36(4):674-97.

(opens in a new window)Gremlin Plays a Key Role in the Pathogenesis of Pulmonary Hypertension.Cahill, E. et al. Circulation. 2012 Feb 21;125(7):920-30.

(opens in a new window)Osteogenic differentiation of mesenchymal stem cells is regulated by osteocyte and osteoblast cells in a simplified bone niche.Birmingham, E. et al. Eur Cell Mater. 2012 Jan 12;23:13-27.

(opens in a new window)The topology design principles that determine the spatiotemporal dynamics of G-protein cascades.Tsyganov, M.A., Kolch, W. & Kholodenko, B.N. Mol Biosyst. 2012 Mar;8(3):730-43.

(opens in a new window)Nambu bracket formulation of nonlinear biochemical reactions beyond mass action kinetics.Frank, T.D. Journal of Nonlinear Mathematical Physics. 2012 Jan; 19(1):81-97.

(opens in a new window)It takes two to tango: signalling by dimeric Raf kinases.Baljuls, A., Kholodenko, B.N. & Kolch, W. Molecular Biosystems. 2013 Apr 5;9(4):551-8.

(opens in a new window)Enhancing the MSC Therapeutic Response: Cell Localization and Support for Cartilage Repair.Bulman, S. et al. Tissue Eng Part B Rev. 2013 Feb;19(1):58-68.

(opens in a new window)Strategies for improved targeting of therapeutic cells: implications for tissue repair.Ansboro S. et al. Eur Cell Mater. 2012 Apr 21;23:310-8; discussion 318-9.

(opens in a new window)Computational approaches for analyzing information flow in biological networks.Kholodenko, B.N., Yaffe, M.B. & Kolch, W. Sci. Signal. 2012 Apr 17;5(220):re1.

(opens in a new window)Instructive reconstruction: A new role for apoptosis in pattern formation.Duffy, D.J. BioEssays. 2012 Jul;34(7):561-4.

(opens in a new window)Signalling by protein phosphatases and drug development: a systems-centered view.Nguyen, L.K. et al. FEBS J. 2013 Jan;280(2):751-65.

(opens in a new window)Bimodal Protein Distributions in Heterogeneous Oscillating Systems.DobrzyDski, M. et al. Computational Methods in Systems Biology 2012; 17-28.

(opens in a new window)Understanding cell fate decisions by identifying crucial system dynamics.Fey, D. et al. New Challenges for Cancer Systems Biomedicine. SIMAI Springer Series. 2012; 83-104

(opens in a new window)Stimulation of BKV DNA replication by NFI-family transcription factorLiang, B. et al. J Virol. 2012 Mar;86(6):3264-75.

(opens in a new window)Mutant K-Ras Activation of the Proapoptotic MST2 Pathway Is Mutant K-Ras Activation of the Proapoptotic MST2 Pathway Is Antagonized by Wild-Type K-RasMatallanas, D. et al. Mol Cell. 2011 Dec 23;44(6):893-906.

(opens in a new window)Switches, Excitable Responses and Oscillations in the Ring1B/Bmi1 Ubiquitination System.Nguyen, L.K. et al. PLoS Comput Biol. 2011 Dec;7(12):e1002317.

(opens in a new window)A heat shock protein and Wnt signalling crosstalk during axial patterning and stem cell proliferation.Duffy, D.J. et al. Developmental Biology. 2012 Feb 15;362(2):271-81.

(opens in a new window)Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modelling.Birtwistle, M.R. et al. PLoS One. 2011;6(11):e27823.

(opens in a new window)NFκB and HIF display synergistic behaviour during hypoxic inflammation.Bruning, U. et al. Cell Mol Life Sci. 2012 Apr;69(8):1319-29.

(opens in a new window)Eukaryotic translation initiation factor 3, subunit a, regulates the extracellular signal-regulated kinase pathway.Xu, T.R. et al. Mol Cell Biol. 2012 Jan;32(1):88-95.

(opens in a new window)Modification of Histones by Sugar β-N-Acetylglucosamine (GlcNAc) Occurs on Multiple Residues, Including Histone H3 Serine 10, and Is Cell Cycle-regulated.Zhang, S. et al. J Biol Chem. 2011 Oct 28; 286(43): 37483–37495.

(opens in a new window)Mesenchymal stem cell inhibition of T-helper 17 differentiation is triggered by cell-cell contact and mediated by prostaglandin E2 via the EP4 receptor.Duffy, M.M. et al. Eur J Immunology. 2011 Oct;41(10):2840-51.

(opens in a new window)A 19S proteasomal subunit cooperates with an ERK MAPK-regulated degron to regulate accumulation of Fra-1 in tumour cells.Pakay, J.L. et al. Oncogene. 2012 Apr 5;31(14):1817-24.

(opens in a new window)MicroRNA-155 Promotes Resolution of Hypoxia-Inducible Factor 1α Activity during Prolonged Hypoxia.Bruning, U. et al. Mol Cell Biol. 2011 Oct;31(19):4087-96.

(opens in a new window)Overexpression of pulmonary extracellular superoxide dismutase attenuates endotoxin-induced acute lung injury.Hassett, P. et al. Intensive Care Med. 2011 Oct;37(10):1680-7.

(opens in a new window)In vitro Characterization of an Electroactive Carbon-Nanotube-Based Nanofiber Scaffold for Tissue Engineering.Mackle, J.N. et al. Macromol Biosc. 2011 Sep 9;11(9):1272-82.

(opens in a new window)Biology using engineering tools: The negative feedback amplifier.Birtwistle, M.R. et al. Cell Cycle. 2011 Jul 1;10(13):2069-76.

(opens in a new window)Gene-eluting stents: non-viral, liposome-based gene delivery of eNOS to the blood vessel wall in vivo results in enhanced endothelialization but does not reduce restenosis in a hypercholesterolemic model.Sharif, F, et al. Gene Ther. 2012 Mar;19(3):321-8.

(opens in a new window)Stochastic processes and mean field systems defined by nonlinear Markov chains: an illustration for a model of evolutionary population dynamics.Frank, T D. Brazilian Journal of Physics. 2011; 41;129.

(opens in a new window)Mesenchymal Stem Cell (MSC) mediated delivery of the Sodium Iodide Symporter (NIS) supports radionuclide imaging and treatment of breast cancer.Dwyer, R.M. et al. Stem Cells. 2011 Jul;29(7):1149-57.

(opens in a new window)Prolactin-stimulated activation of ERK1/2 mitogen-activated protein kinases is controlled by PI3-kinase/Rac/PAK signalling pathway in breast cancer cells.Aksamitiene, E. et al. Cell Signal. 2011 Nov;23(11):1794-805.

(opens in a new window)Behavioral dynamics of the affordance "graspable".Lopresti-Goodman, S.M., Turvey, M.T. & Frank, T.D. Attention, Perception, and Psychophysics. 2011 Aug;73(6):1948-65.

(opens in a new window)Unifying mass-action kinetics and Newtonian mechanics by means of Nambu brackets.Frank, T.D. Journal of Biological Physics. 2011 Sep;37(4):375-85.

(opens in a new window)Rate of entropy production as a physical selection principle for mode-mode transitions in non-equilibrium systems: with an application to a non-algorithmic dynamic message buffer.Frank, T.D. European Journal of Scientific Research. 2011

(opens in a new window)Developing cell-specific antibodies to endothelial progenitor cells using avian immune phage display technology.Bowes, T. et al. Journal of biomolecular screening. 2011 Aug;16(7):744-54.

(opens in a new window)Stem Cell Research & Therapy marks its first anniversary.Locke, P., O'Brien, T. & Tuan, R.S. Editorial Stem Cell Research & Therapy. 2011; 2(3): 22.

(opens in a new window)Inhibition of human BK polyomavirus replication by small non-coding RNAs.Tikhanovich, I. et al. J Virol. 2011 June; 85(14):6930-6940.

(opens in a new window)c-Myc regulates RNA splicing of the A-Raf kinase and its activation of the ERK pathway.Rauch, J. et al. Cancer Research. 2011 Jul 1;71(13):4664-74.

(opens in a new window)Lentiviral Vector Mediated modification of Mesenchymal Stem Cells & enhanced survival in an in vitro mode of Ischaemia.McGinley, L. et al. Stem Cell Research & Therapy. 2011 Mar 7;2(2):12.

(opens in a new window)Differential miRNA expression in omental adipose tissue and in the circulation of obese patients identifies novel metabolic biomarkers.Heneghan, H.M. et al. J Clin Endocrinol Metab. 2011 May;96(5):E846-50.

(opens in a new window)Distinct noise-controlling roles of multiple negative feedback mechanisms in a prokaryotic operon system.Nguyen, L.N. & Kulasiri, D. IET Syst Biol. 2011 Mar;5(2):145-56.

(opens in a new window)Mesenchymal Chondroprogenitor Cell Origin, Isolation and Therapeutic Potential.O'Sullivan, J. et al. Stem Cell Research & Therapy. 2011 Feb 18;2(1):8.

(opens in a new window)Raf Kinase Inhibitor Protein RKIP enhances signalling by Glycogen Synthase Kinase-3 b.Al-Mulla, F. et al. Cancer Res. 2011 Feb 15;71(4):1334-43.

(opens in a new window)Small ubiquitin-related modifier (SUMO)-1 promotes glycolysis in hypoxia.Agbor, T.A. et al. Biol Chem. 2011 Feb 11;286(6):4718-26.

(opens in a new window)Spatial regulation of RhoA activity during pancreatic cancer cell invasion driven by mutant p53.Timpson, P. et al. Cancer Research. 2011 Feb 1;71(3):747-57.

(opens in a new window)Functionalized scaffold mediated interleukin-10 gene delivery significantly improves survival rates of stem cells in vivo.Holladay, C. et al. Mol Ther. 2011 May;19(5):969-78.

(opens in a new window)Virial theorem and non-equilibrium canonical-dissipative distributions characterizing Parkinson tremor.Frank, T.D. International Journal of Modern Physics. 2011; 25(2): 243-253

(opens in a new window)A Temporal Gene Delivery System based on Fibrin Microshpheres.Kulkarni, M.M. et al. Mol Pharm. 2011 Apr 4;8(2):439-46.

(opens in a new window)The secret life of kinases: functions beyond catalysis.Rauch, J. et al. Cell Commun Signal. 2011 Oct 28;9(1):23.

(opens in a new window)Raf family kinases: old dogs have learned new tricks.Matallanas, D. et al. Genes & Cancer. 2011 Mar;2(3):232-60.

(opens in a new window)Stem Cell Therapy for Cardiac Disease.Flynn, A. & O'Brien, T. Expert Opinion on Biological Therapy. 2011 Feb;11(2):177-87.

(opens in a new window)Regulation of gene expression by carbon dioxide.Taylor, C.T., & Cummins, E.P. J Physiol. 2011 Feb 15;589(Pt 4):797-803.

(opens in a new window)Understanding movement during performance: a recurrence quantization approach.Demos, A.P., Frank, T.D. & Chaffin, R. International Symposium on Performance Science. 2011 Jan;

(opens in a new window)An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells.Santra, T, Kholodenko B.N. & Kolch, W. Advances in Systems Biology, Advances in Experimental Medicine and Biology. 2012;736:59-80.

(opens in a new window)Evolution of Bet-Hedging Mechanisms in Cell Cycle and Embryo Development Stimulated by Weak Linkage of Stochastic Processes.Dobrzyński, M. et al. Cell Cycle in Development. 2011;53:11-30.

(opens in a new window)The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells.. Meesbah, J. et al. BMC Molecular Biology. 2010 Dec 31;11:103.

(opens in a new window)The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier.. Oliver, E. et al. Science Signalling. 2010 Dec 21;3(153):ra90.

(opens in a new window)Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers.. Dakna, M. et al. BMC Bioinformatics. 2010 Dec 10;11:594.

(opens in a new window)Nutrient exposure of chemotactic organisms in small scale turbulent flows.. Muñoz-García, J., Neufeld, Z. & Torney, C. New Journal of Physics. 2010 October; 12

(opens in a new window)Lentiviral vector-mediated knockdown of the neuroglycan 2proteoglycan or expression of neurotrophin-3 promotes neurite outgrowth in a cell culture model of the glial scar.. Donnelly, E.M. et al. Journal of Gene Medicine. 2010 Nov;12(11):863-72.

(opens in a new window)Mesenchymal Stem Cells Overexpressing Ephrin-B2 Rapidly Adopt an Early Endothelial Phenotype with Simultaneous Reduction of Osteogenic Potential.. Duffy, G.P. et al. Tissue Engineering Part A. 2010 Sep;16(9):2755-68.

(opens in a new window)Hydroxylase inhibition attenuates colonic epithelial secretory function and ameliorates experimental diarrhea.. Ward, J.B. ety al. FASEB Journal. 2011 Feb;25(2):535-43.

(opens in a new window)NF-κB links CO2 sensing to innate immunity and inflammation in mammalian cells.. Cummins, E.P. et al. J Immunol. 2010 Oct 1;185(7):4439-45.

(opens in a new window)Ancient atmospheres and the evolution of oxygen sensing via the hypoxia inducible factor in metazoans.. Taylor, C.T. & McElwain, J.C. Physiology. 2010 Oct;25(5):272-9.

(opens in a new window)The OARSI histopathology initiative: recommendations for histological assessments of osteoarthritis in sheep and goats.. Little, C.B., et al. Osteoarthritis and Cartilage. 2010 Oct;18 Suppl 3:S80-92.

(opens in a new window)Functional roles of multiple feedback loops in extracellular signal-regulated kinase and Wnt signalling pathways that regulate epithelial-mesenchymal transition.. Shin, S.Y. et al. Cancer Res. 2010 Sep 1;70(17):6715-24.

(opens in a new window)Introduction to Series on Mesenchymal Stromal (Stem) Cells-MSCs.. O'Brien, T. & Barry, F. Human Gene Therapy. 2010 Sep;21(9):1037-8.

(opens in a new window)Recommendations for biomarker identification and qualification in clinical proteomics.. Mischak, H. et al. Sci Transl Med. 2010 Aug 25;2(46):46ps42.

(opens in a new window)Potential of rat bone marrow-derived mesenchymal stem cells as vehicles for delivery of neurotrophins to the Parkinsonian rat brain.. Moloney, T.C. et al. Journal of Brain Research. 2010 Nov 4;1359:33-43.

(opens in a new window)Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models.. Vera, J. et al. Mol Biosyst. 2010 Nov;6(11):2174-91.

(opens in a new window)On-chip immunoprecipitation for protein purification.. Sandison, M.E. et al. Lab Chip. 2010 Oct 21;10(20):2805-13.

(opens in a new window)Hypoxia, innate immunity and infection in the lung.. Schaible, B., Schaffer, K.E. & Taylor, C.T. Respiratory Physiology and Neurobiology. 2010 Dec 31;174(3):235-43.

(opens in a new window)Stabilization of hypoxia inducible factor-1alpha protein in hypoxia occurs independently of mitochondrial reactive species production oxygen.. Chua, Y.L. et al. J Biol Chem. 2010 Oct 8;285(41):31277-84.

(opens in a new window)Monitoring of cell oxygenation and responses to metabolic stimulation by intracellular oxygen sensing technique.. Zhdanov, A.V. et al. Integrative Biology. 2010 Sep;2(9):443-51.

(opens in a new window)Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease.. Good, D.M. et al. Mol Cell Proteomics. 2010 Nov;9(11):2424-37.

(opens in a new window)Formation of Intracellular Concentration Landscapes by Multisite Protein Modification.. Munoz-Garc, J., Kholodenko, B.N. & Neufeld, Z. Biophys J. 2010 Jul 7;99(1):59-66.

(opens in a new window)Loss of Prolyl Hydroxylase-1 Protects Against Colitis Through Reduced Epithelial Cell Apoptosis and Increased Barrier Function.. Tambuwala, M.M. et al. Gastroenterology. 2010 Dec;139(6):2093-101.

(opens in a new window)Extracellular calcium depletion transiently elevates oxygen consumption in neurosecretory PC12 cells through activation of mitochondrial Na(+)/Ca(2+) exchange.. Zhdanov, A.V. et al. Biochimica et biophysica Acta. 2010 Sep;1797(9):1627-1637.

(opens in a new window)The RASSF8 candidate tumor suppressor inhibits cell growth and regulates the Wnt and NF-κB signalling pathways.. Lock, F.E. et al. Oncogene. 2010 Jul 29;29(30):4307-4316.

(opens in a new window)Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics.. Nakakuki, T. et al. Cell. 2010 May 28;141(5):884-96.

(opens in a new window)PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells.. Aksamitiene, E. et al. Cell Signal. 2010 Sep;22(9):1369-78.

(opens in a new window)Engraftment, migration and differentiation of neural stem cells in the rat spinal cord following contusion injury.. McMahon, S.S. et al. Cryotherapy. 2010 May;12(3):313-25.

(opens in a new window)In vitro differentiation potential of human embryonic versus adult stem cells.. Rooney, G.E. et al. Regenerative Medicine. 2010 MAy; 5(3)

(opens in a new window)Bolus Delivery of Mesenchymal Stem Cells to Injured Vasculature in the Rabbit Carotid Artery Produces a Dysfunctional Endothelium.. O'Shea, C.A. et al. Tissue Eng Part A. 2010 May;16(5):1657-65.

(opens in a new window)Host-specific replication of BK virus DNA in mouse cell extracts is independently controlled by DNA polymerase alpha-primase and inhibitory activities.. Tikhanovich, I. & Nasheuer, H.P. Journal of Virology. 2010 Jul;84(13):6636-44.

(opens in a new window)Survival and Immunogenicity of Mesenchymal Stem Cells from the Green Fluorescent Protein Transgenic Rat in the Adult Rat Brain.. Moloney, T.C. et al. Neurorehabilitation and Neural repair. 2010 Sep;24(7):645-56.

(opens in a new window)Identification of potential HLA class I and class II epitope precursors associated with heat shock protein 70 (HSPA).. Stocki, P. et al. Cell Stress Chaperones. 2010 Sep;15(5):729-41.

(opens in a new window)Inferring Signalling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species.. Tian-Rui, X.U. et al. Sci. Signal. 2010 Mar 16;3(113):ra20

(opens in a new window)Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.. Fleming, R.M. et al. Journal of Theoretical Biology. un 7;264(3):683-92.

(opens in a new window)Genetically Modified Mesenchymal Stem Cells and Their Clinical Potential in Acute Cardiovascular Disease.. Griffin, M, et al. Discovery Medicine. 2010 Mar;9(46):219-23.

(opens in a new window)Angiogenesis and blood vessel stability in inflammatory arthritis.. Kennedy, A. et al. Arthritis & Rheumatism. 2010 Mar;62(3):711-21.

(opens in a new window)Heterogeneous nuclear ribonucleoprotein H blocks MST2-mediated apoptosis in cancer cells by regulating A-Raf transcription.. Rauch, J. et al. Cancer Res. 2010 Feb 15;70(4):1679-88.

(opens in a new window)Co-operation between Raf-1 and Akt pathways for the inhibition of RASSF1A-MST2-triggered apoptosis.. Romano, D. et al. Cancer Res. 2010 Feb; 1,70(3): 1195-1203

(opens in a new window)Proapoptotic Kinase MST2 Coordinates Signalling Crosstalk between RASSF1A, Raf-1, and Akt.. Romano, D. et al. Cancer Res. 2010 Feb 1;70(3):1195-203.

(opens in a new window)Potential Role of Mesenchymal Stem Cells (MSCs) in the Breast Tumor Microenvironment: Stimulation of Epithelial to Mesenchymal Transition (EMT).. Martin, F.T. et al. Breast Cancer Research and Treatment. 2010 Nov;124(2):317-26.

(opens in a new window)Enhanced lipoplex-mediated gene expression in mesenchymal stem cells using reiterated nuclear localization sequence peptides.. Hoare, M. et al. Journal of Gene Medicine. 2010 Feb;12(2):207-18.

(opens in a new window)The Bcr-Abl kinase regulates the actin cytoskeleton via a GADS/Slp-76/Nck1 adaptor protein pathway.. Preisinger, C. & Kolch, W. Cell Signal. 2010 May;22(5):848-56.

(opens in a new window)Behavior of Human Mesenchymal Stem Cells in Fibrin-Based Vascular Tissue Engineering Constructs.. O'Cearbhaill, E.D. et al. Annals of Biomedical Engineering. 2010 Mar;38(3):649-57.

(opens in a new window)General Practioners' Attitudes and Preparedness toward Clinical Decision Support in e-Prescribing (CDS-dP) Adoption in the West of Ireland: a cross sectional study.. Peng Hor, C. et al. BMC Med Inform Decis Mak. 2010 Jan 12;10:2.

(opens in a new window)Alterations in oxidative gene expression in equine skeletal muscle following exercise and training.. Eivers, S.S. et al. Physiological Genomics. 2010 Jan 8;40(2):83-93.

(opens in a new window)New druggable targets in the Ras pathway.. Matallanas, D.& Crespo, P. Current Opinion in Molecular Therapeutics. 2010 Dec;12(6):674-83.

(opens in a new window)Compassionate use of interventions: results of a European Clinical Research Infrastructures Network (ECRIN) survey of ten European countries.. Whitfiel, K. et al. Cohen-Haguenauer, O. et al. Trials. 2010 Nov 12;11:104.

(opens in a new window)Relevance of an Academic GMP Pan-European Vector Infra-structure (PEVI).. Curr Gene Ther. 2010 Dec;10(6):414-22.

(opens in a new window)Signalling over a distance: gradient patterns and phosphorylation waves within single cells.. Muñoz-García, J. & Kholodenko, B.N. Biochem Soc Trans. 2010 Oct;38(5):1235-41.

(opens in a new window)Translation of science to surgery: linking emerging concepts in biological cartilage repair to surgical intervention.. Moran, C.J. et al. J Bone Joint Surg Br. 2010 Sep;92(9):1195-202.

(opens in a new window)Mesenchymal Stem Cells and Osteoarthritis: Remedy or Accomplice?. Coleman, C.M. et al. Hum Gene Ther. 2010 Oct;21(10):1239-50.

(opens in a new window)Functional proteomics to dissect tyrosine kinase signalling pathways in cancer.. Kolch, W. & Pitt A. Nature Reviews Cancer. 2010 Sep;10(9):618-29.

(opens in a new window)Advances in mesenchymal stem cell-mediated gene therapy for cancer.. Dwyer, R.M. et al. Stem Cell Res Ther. 2010 Aug 9;1(3):25.

(opens in a new window)Signalling Ballet in Space and Time.. Kholodenko, B.N., Hancock, J.F. & Kolch, W. Nature Reviews Molecular Cell Biology 11. 2010 Jun;11(6):414-26.

(opens in a new window)Non-viral gene therapy for myocardial engineering.. Holladay, C., O'Brien, T. & Pandit, A. Wiley Interdiscip Rev Nanomed Nanobiotechnol. May-Jun 2010;2(3):232-48.

(opens in a new window)Hypoxia: an alarm signal during intestinal inflammation.. Colgan, S.P. & Taylor, C.T. Nat Rev Gastroenterol Hepatol. 2010 May;7(5):281-7.

(opens in a new window)A-Raf.. Rauch J, Kolch W. AfCS-Nature Molecule Pages. 2010 April;

(opens in a new window)Welcome to Stem Cell Research & Therapy.. Donnelly, A. et al. Stem Cell Research & Therapy. 2010 March; 1,1

(opens in a new window)α Cell Protection by Inhibition of iNOS through Lentiviral Vector-Based Strategies.. Hynes, S.O., McCabe, C. & O'Brien, T. Methods Mol Biol. 2007 Sep;37(1):38-47.

(opens in a new window)Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions.Schilling, M. et al. Mol Syst Biol. 2009;5:334.

(opens in a new window)Gram stain/aolc screening for detection of catheter related bloodstream infection.Zach, J. et al. Journal of Infection. 2010 Mar;60(3):254-5.

(opens in a new window)Aggregation of chemotactic organisms in a differential flow.Muñoz-García, J. & Neufeld, Z. Physical Review. 2009 Dec;80(6 Pt 1):061902.

(opens in a new window)Cell fate decisions are specified by the dynamic ERK interactome.von Kriegsheim, A. et al. Nature Cell Biology. 2009 Dec;11(12):1458-64.

(opens in a new window)MST kinases monitor actin cytoskeletal integrity and signal via c-Jun N-terminal kinase stress-activated kinase to regulate p21Waf1/Cip1 stability.Densham, R.M. et al. Mol Cell Biol. 2009 Dec;29(24):6380-90.

(opens in a new window)Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway.Orton, R.J. et al. BMC Syst Biol. 2009 Oct 5;3:100.

(opens in a new window)Generation of antioxidant adenovirus gene transfer vectors encoding CuZnSOD, MnSOD, and catalase.Duffy, A.M., O'Brien, T. & McMahon, J.M. Methods in Molecular Biology. 2010;594:381-93.

(opens in a new window)HPLC purification of adenoviral vectors.Eglon, M., McGrath, B. & O'Brien, T. Methods in Molecular Biology. 2010;594:395-408.

(opens in a new window)Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli.Fleming, R.M., Thiele, I. & Nasheuer, H.P. Biophysical Chemistry. 2009 Dec;145(2-3):47-56.

(opens in a new window)RASSF2 associates with and stabilizes the proapoptotic kinase MST2.Cooper, W.N. et al.Oncogene. 2009 Aug 20;28(33):2988-98.

(opens in a new window)Ionizing radiation-dependent and independent phosphorylation of the 32-kDa subunit of replication protein A during mitosis.Holger, S. et al. Nucleic Acids Research. 2009 Oct;37(18):6028-41.

(opens in a new window)Exploration of homodimer receptor: homodimer protein interactions.Vera, J. et al. Int J Bioinform Res Appl. 2009;5(4):447-57.

(opens in a new window)RAN GTPase is a RASSF1A effector involved in controlling microtubule organization.Dallol, A. et al. Cell Cycle. 2009 Jul 28;19(14):1227-32.

(opens in a new window)Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle.Kaimachnikov, N.P. & Kholodenko, B.N. FEBS Journal. 2009 Aug;276(15):4102-18.

(opens in a new window)The C-terminus of Raf-1 acts as a 14-3-3-dependent activation switch.Dhillon, A.S. et al. Cell Signal. 2009 Nov;21(11):1645-51.

(opens in a new window)Microfluidic single cell arrays to interrogate signalling dynamics of individual, patient-derived hematopoietic stem cells.Faley, S.L. et al. Lab Chip. 2009 Sep 21;9(18):2659-64.

(opens in a new window)Angiogenin protects motoneurons against hypoxic Injury.Sebastia, J. et al. Cell Death and Differentiation. 2009 May; 16:1238-1247

(opens in a new window)Multiple roles of the NF-kappaB signalling pathway regulated by coupled negative feedback circuits.Kim, D., Kolch, W. & Cho, K.H. FASEB J

(opens in a new window)Systems-level interactions between insulin-EGF networks amplify mitogenic signalling.Borisov, N. et al. Molecular Systems Biology, 2009; 5: 256.

(opens in a new window)XRCC1 interacts with the p58 subunit of DNA Pol alpha-primase and may coordinate DNA repair and replication during S phase.Lévy, N. et al. Nucleic Acids Research. 2009 Jun;37(10):3177-88.

(opens in a new window)Positional information generated by spatially distributed signalling cascades.Munoz-Ga 2009 Sep;23(9):2796-802.rcia, J., Neufeld, Z. & Kholodenko, B.N. PLoS Computational Biology. 2009 Mar;5(3):e1000330.

(opens in a new window)Restriction of human polyomavirus BK virus DNA replication in murine cells and extracts.Mahon, C. et al. J Virol. 2009 Jun;83(11):5708-17.

(opens in a new window)Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor.Suenaga, A. et al. Biophysical Journal. 2009 Mar 18;96(6):2278-88.

(opens in a new window)Spatially distributed cell signalling.Kholodenko, B.N. FEBS Letters. 2009 Dec 17;583(24):4006-12.

(opens in a new window)Journeys to high altitude-risks and recommendations for travellers with preexisting medical conditions.Mieske, K., Flaherty, G. & O'Brien, T. Journal of Travel Medicine. Jan-Feb 2010;17(1):48-62.

(opens in a new window)Liposomal Gene Delivery Mediated by Tissue-Engineered Scaffolds: Trends Biotechnology.Kulkarni M. et al. Trends in Biotechnology. 2010 Jan;28(1):28-36.

(opens in a new window)Endocytosis and signalling: a meeting with mathematics.Birtwistle MR, Kholodenko BN. Mol Oncol. 2009 Aug;3(4):308-20.

(opens in a new window)Genome Stability and Human Diseases.Nasheuer, H.P. Subcell Biochem. 2010.

(opens in a new window)The use of transgenic mice in cancer and genome stability research.Conmy, S. & Nasheuer, H.P. Subcell Biochem. 2010;50:325-36.

(opens in a new window)Eukaryotic single-stranded DNA binding proteins: central factors in genome stability.Broderick, S. et al. Subcell Biochem. 2010;50:143-63.